On the existence of a hysteresis loop in open and closed end pores

We have studied the adsorption of argon at 87 K in slit pores of finite length with a smooth graphitic potential, open at both ends or closed at one end. Simulations were carried out using conventional GCMC (grand canonical Monte Carlo) or kMC (kinetic Monte Carlo) in the canonical ensemble with extremely long Markov chain, of at least 2 × 10⁸ configurations; selected simulations with much longer Markov chains do not show any change in the results. When the pore width is in the micropore range (0.65 nm), type I isotherms are obtained for both pore models and for both simulation methods. However, wider pores (1, 2 and 3 nm in width) all exhibit hysteresis loops in the GCMC simulations, while in the canonical ensemble simulations, the isotherms pass through a sigmoid van der Waals type loop in the transition region. This loop locates the true equilibrium transition. For the pores with one closed end, this transition is close to, or coincides with, the adsorption branch of the GCMC hysteresis loop, but for the open-ended pores, it is more closely associated with the desorption branch. In a separate study of adsorption hysteresis in an infinitely long slit pore, using both simulation techniques, the van der Waals loop follows the adsorption branch of the GCMC isotherm to the transition, then reverts to a long vertical section that falls midway between the two hysteresis branches and finally moves to the desorption transition close to the evaporation pressure. An examination of molecular distributions inside the pores reveals two coexisting phases in the canonical simulations, whereas in the grand canonical simulations, the molecules are uniformly distributed along the length of the pores.     

Methane storage in homogeneous armchair open-ended single-walled boron nitride nanotube triangular arrays: a grand canonical Monte Carlo simulation study

The physisorption of methane in homogeneous armchair open-ended SWBNNT triangular arrays was evaluated using grand canonical ensemble Monte Carlo simulation for tubes 11.08, 13.85, 16.62, and 19.41 ? [(8,8), (10,10), (12,12), and (14,14), respectively] in diameter, at temperatures of 273, 298, 323, and 373 K, and at fugacities of 0.5-9.0 Mpa. The intermolecular forces were modeled using the Lennard-Jones potential model. The absolute, excess, and delivery adsorption isotherms of methane were calculated for the various boron nitride nanotube arrays. The specific surface areas and the isosteric heats of adsorption, Q(st), were also studied, different isotherm models were fitted to the simulated adsorption data, and the model parameters were correlated. According to the results, it is possible to reach 108% and 140% of the US Department of Energy's target for CH(4) storage (180 v/v at 298 K and 35 bar) using the SWBNNT array with nanotubes 16.62 and 19.41 ? in diameter, respectively, as adsorbent. The results show that for a van der Waals gap of 3.4 ?, there is no interstitial adsorption except for arrays containing nanotubes with diameters of >15.8 ?. Multilayer adsorption starts to occur in arrays containing nanotubes with diameters of >16.62 ?, and the minimum pressure required for multilayer adsorption is 1.0 MPa. A brief comparison of the methane adsorption capacities of single-walled carbon and boron nitride nanotube arrays was also performed.     

Molecular simulation of shale gas adsorption and diffusion in inorganic nanopores

We studied the structural and dynamical properties of methane and ethane in montmorillonite (MMT) slit pore of sizes 10, 20 and 30 Å using grand canonical Monte Carlo and classical molecular dynamics (MD) simulations. The isotherm, at 298.15 K, is generated for pressures up to 60 bar. The molecules preferentially adsorb at the surface as indicated by the density profile. In case of methane, we observe only a single layer, at the pore wall, whose density increases with increasing pressure. However, ethane also displays a second layer, though of low density in case of pore widths 20 and 30 Å. In-plane self-diffusion coefficient, D_‖, of methane and ethane is of the order of 10^? 6 m²/s. At low pressure, D_‖ increases significantly with the pore size. However, D_‖ decreases rapidly with increasing pressure. Furthermore, the effect of pore size on D_‖ diminishes at high pressure. Ideal adsorbed solution theory is used to understand the adsorption behaviour of the binary mixture of methane (80%) and ethane (20%) at 298.15 K. Furthermore, we calculate the selectivity of the gases at various pressures of the mixture, and found high selectivity for ethane in MMT pores. However, selectivity of ethane decreases with increase in pressure or pore size.     

Molecular dynamics simulation of water confined in a nanopore of amorphous silica

Molecular dynamics simulations are performed to study the transport and structural properties of water confined in a cylindrical silica nanopore. The pore wall is amorphous and mimics a typical mesoporous silica material. The diameters of silica pores studied are 4.75, 9.51, 20 and 25 Å. The self-diffusion of water calculated decreases with pore size and indicates much slower transport compared to the bulk phase. Strong adsorption of water to the silica wall is observed in the density profiles, indicating the hydrophilic nature of the wall. The hydrogen-bonding network is strongly affected by water–silica wall interaction. The average number of hydrogen bonds per water decreased with decreasing pore diameter.     

Controlling activation barrier by carbon nanotubes as nano-chemical reactors

The oxidative addition of primary amine on a monocyclic phospholane was studied in confined conditions. This one-step chemical reaction has been investigated using the DFT technique to elucidate the role of confinement in carbon nanotubes on the reaction. Calculations were carried out by a progressive increase of the nanotube diameters from 10 Å to 15 Å in order to highlight the dependence of the reactivity on the nanotube diameter. First, single point investigations were dedicated to the study of reactants, transition states, and products placed in the different nanotubes while keeping their optimized structure as free compounds. Second, all studied compounds were relaxed inside nanotubes and their geometries were fully optimized. Within these approaches, we proved that the activation barrier could be controlled depending on the confinement, generating a well-controlled catalysis process.     

Modelling Gas Adsorption in Slit-Pores Using Monte Carlo Simulation

Abstract

We discuss the use of Monte Carlo simulation to model the equilibrium adsorption of gases in slit pores. Databases of adsorption isotherms have been calculated for nitrogen, carbon-monoxide, methane and carbon-dioxide for a range of pressures, pore widths and temperatures. We discuss the implications of these results for materials characterisation procedures based on gas adsorption data.     

Simple benzene derivatives adsorption on defective single-walled carbon nanotubes: a first-principles van der Waals density functional study

We have investigated the interaction between open-ended zig-zag single-walled carbon nanotube (SWCNT) and a few benzene derivatives using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such sp ²-like materials are typically investigated using conventional DFT methods, which significantly underestimate non-local dispersion forces (vdW interactions), therefore affecting interactions between respected molecules. Here, we considered the vdW forces for the interacting molecules that originate from the interacting π electrons of the two systems. The ?0.54 eV adsorption energy reveals that the interaction of benzene with the side wall of the SWCNT is typical of the strong physisorption and comparable with the experimental value for benzene adsorption onto the graphene sheet. It was found that aromatics are physisorbed on the sidewall of perfect SWCNTs, as well as at the edge site of the defective nanotube. Analysis of the electronic structures shows that no orbital hybridization between aromatics and nanotubes occurs in the adsorption process. The results are relevant in order to identify the potential applications of noncovalent functionalized systems.

Acetylcholine receptor pore permeability studied by molecular dynamics simulation

A dynamic model of the closed-state pore of an acetylcholine receptor (five M2 α-helices stabilized with a (CH₂)₁₀₅ ring) is used to examine the migration of uncharged and charged probe particles equivalent to a hexahydrated sodium ion (van der Waals diameter 7.27 Å) propelled by varied external force along the channel axis. Ion movement through the pore is hindered by steric constraints and electrostatic interactions. The van der Waals gate is formed by helix residues 13′ (A-Val255, B-Val261, C-Val269, D-Val255, and E-Ile264), whereas the negatively charged residues in the upper part of the channel are important for ion selectivity.     

Molecular insight into adsorption affinities of Carmustine drug on boron and nitrogen doped functionalized single-walled carbon nanotubes using density functional theory including dispersion correction calculations and molecular dynamics simulation

Abstract

We report a quantum mechanics calculation and molecular dynamics simulation study of Carmustine drug (BNU) adsorption on the surface of nitrogen (N) and boron (B) doped-functionalized single-walled carbon nanotubes. The stability of the optimized complexes is determined on the basis of relative adsorption energy (ΔE_ads). The ΔE_ads results claim that drug molecule tends to adsorb on the nitrogen and boron doped functionalized tubes with the energy values in the range of ?61.177 to ?95.806?kJ/mol. Based on the obtained results, it is observed that N-doping compared with B-doping has improved more effectively drug absorption on the surface of functionalized nanotube. The results of Atoms in Molecule calculations indicate that drug adsorbs molecularly via hydrogen bonds interactions on the surface doped-functionalized carbon nanotubes. Moreover, molecular dynamics simulation is performed to investigate the dynamics behavior of the drug molecules on the nitrogen-doped functionalized carbon nanotube (f-NNT) and functionalized carbon nanotube (f-CNT). The higher average calculated electrostatic and van der Waals energies as well as higher number of intermolecular hydrogen bonds in BNU-f-NNT in comparison with BNU-f-CNT model suggest the more effectual interaction between drug molecules and nitrogen-doped functionalized carbon nanotube.

Communicated by Ramaswamy H. Sarma     

Altered nuclear pore diameters in G1-arrested cells of the yeast Saccharomyces cerevisiae.

Nuclear pores in cells of the yeast Saccharomyces cerevisiae were examined by using the freeze-fracture technique. Nuclear pore diameters in actively growing cells appear to be exclusively of the normal diameter (75 to 115 nm), whereas some pore diameters in abnormally small G1-arrested cells produced by nitrogen starvation are unusually wide (120 to 160 nm). There may be a correlation between nuclear pore size and nuclear envelope size, the larger pores tending to occur in the smaller envelopes. The finding suggests that nuclear pore diameter may not function in regulating the flow of informational molecules from nucleus to cytoplasm, but may be implicated in regulating the flow of substrates into the nucleus.     

Mechanism of methane adsorption on groove space in organic matter surface

Organic matter plays an important role in methane adsorption in shale. Pore surface of organic matter is usually rough and uneven, which results in a large amount of groove space on the pore surface. Thus, the influence of groove space on the adsorption capacity of methane in shale cannot be neglected. Nanoscale pore structures of the organic-rich shale in the Longmaxi Formation were investigated by low-pressure nitrogen gas adsorption as a basis for constructing models. We simplified the internal groove space into triangular prisms with different angles. The grand canonical Monte Carlo simulation and molecular dynamics simulation were used to analyse the methane molecule adsorption behaviour in pores. The results showed that the pore morphology of organic-rich shale in the Longmaxi Formation was mainly slit-shaped pores. The excess adsorption isotherms showed good agreement between experiment and simulation, indicating that the model is suitable and reliable. Methane molecules can enter into the groove space with an opening size of 0.738 nm, while they fail to enter into groove spaces with an opening size less than 0.492 nm. This understanding has important significance for the study of the adsorption characteristics of organic pores which have undergone multiple evolutions in geological history.     

Exploring the effect of confinement on water clusters in carbon nanotubes

Using armchair-type single-walled carbon nanotubes (SWCNTs) of different sizes as model compounds for lignite, the effect of water molecule confinement on the water-holding capacity of lignite pores was investigated. Results indicated that the water-holding capacity of pores with diameters of <10 nm was eight times larger than that of pores with diameters of 100 nm. The configuration of the cluster of water molecules in each SWCNT and the binding energy between each SWCNT and the water molecules within it were calculated by means of density functional theory using a hybrid functional: M06-2X/6-311+G**, 6-31G*. The results prove that the configurations of the water molecules in the SWCNTs are very different to their configuration in the unconfined state. In vacuum, the cluster of three water molecules adopted a trimer configuration, while they presented a linear configuration in the 6.78 Å SWCNT. Similarly, in vacuum, the cluster of five water molecules formed a five-membered ring, while they favored a linear configuration in the 6.78 Å SWCNT, a zigzag configuration in the 8.14 Å SWCNT, and a trimer?+?1?+?1 configuration (i.e., a trimer plus two isolated water molecules) in the 9.49 Å, 10.85 Å, and 13.75 Å SWCNTs. There was found to be a degree of competition between the coupling energy of the water molecules with the SWCNT and the hydrogen bonding among the water molecules. When the diameter of the SWCNT was >1 nm, the hydrogen bonding among the water molecules dominated, while the coupling energy of the water molecules with the SWCNT amounted to only 30–40% of the total interaction energy of the water molecules.

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Graphical Abstract Computed equilibrium structures of five water molecules confined in SWCNTs with diameters of 6.78 Å, 8.14 Å, 9.49 Å, 10.85 Å, and 13.75 Å, and in vacuum

     

The influence of nicotine on pioglitazone encapsulation into carbon nanotube: the investigation of molecular dynamic and density functional theory

In this work, molecular dynamics simulations of the insertion of pioglitazone into the nanotube with chirality (10, 10) at 400 K and 1 bar in the presence and absence of nicotine molecules and in different drug concentrations have been studied. The main aim is consideration of the effect of nicotine in the drug encapsulation process. The results indicate that encapsulation of pioglitazone could be attributed to the water flow via van der Waals and hydrophilic interactions. Because of the existence of the partial π–π interactions between aromatic rings of pioglitazone and the conjugated aromatic rings of nanotube, pioglitazone molecule can enter inside the nanotube. Some physical properties such as hydrogen bonding, number of contacts, also, the diffusion coefficient of the pioglitazone and water molecules, and variation of the center of mass have been calculated during the simulation. Furthermore, computing the electronic structure has also been done on model systems for quantitative determination of the adsorption energy (E_ads). The B3LYP/6-31G* level calculations on four different configurations of pioglitazone/carbon nanotube (CNT) and nicotine/CNT show that the interaction of drug with the inside of the nanotube is stronger than the other forms.     

Pressure effects in confined nanophases

In this article, we review how pressure effects in pores affect both the physics of the confined fluid and the properties of the host porous material. Molecular simulations in which high-pressure effects were observed are first discussed; we will see how the strong dependence on bulk phase pressure of the freezing temperature of a fluid confined in nanopores can be explained by important variations of the pressure within the pore. We then discuss recent works in which direct calculations of the pressure tensor of fluids confined in pores provide evidence for large pressure enhancements. Finally, practical applications of these pressure effects in which gas adsorption in microporous solids (pore size < 2 nm) was found to enhance their mechanical properties by increasing the elastic modulus by a factor 4 are discussed.     

Specific Surface Area and Specific Pore Volume Distribution of Tobacco

The specific surface area and the specific pore volume distribution of Japanese tobaccos were measured by means of the low temperature gas adsorption technique utilizing the B.E.T. and the Inkley methods. The specific surface area and the specific pore volume of the micropores less than 300 Å in diameter varied from 6,000 to 17,000 cm²/g and from 0.0012 to 0.0036 cm³/g, respectively, with types of curing in the ascending order of the sun cured, the flue cured and the air cured tobaccos. The both specific values were increased by extracting the tobaccos with water greatly in the case of the flue cured, while slightly in the case of the air cured tobaccos, suggesting that the effect of the curings on the specific values were due to differences in the content of low molecular components. Effectiveness of puffing was also shown. The specific surface area was linearly correlated with the specific volume of the micropores less than 300 Å in diameter, the constant term showing that contribution of the larger pores more than 300 Å in diameter to the specific surface area of tobacco was insignificant.     

Effect of chirality,length and diameter of carbon nanotubes on the adsorption of 20 amino acids: a molecular dynamics simulation study

We carried out molecular dynamics simulations to study the adsorption of all the 20 amino acids (AAs; aromatic, polar and non-polar) on the surface of chiral, zigzag and armchair single-walled carbon nanotubes. The adsorption was occurring in all systems. In the aromatic AAs, the π–π stacking and the semi-hydrogen bond formation cause a strong interaction with the carbon nanotubes (CNTs). We also investigated the chirality, length and diameter dependencies on adsorption energies. We found that all AAs have more tendency to adsorption on the chiral and zigzag CNTs over the armchair. The results show that increasing both the diameter and the length causes the enhancement of the adsorption energy. But, the effect of the length is more than of the diameter. For example, the adsorption energy of Trp on the surface of CNT (4,1), with 2 nm length, is 20.4 kcal/mol. When the length of CNT becomes twice, the adsorption energy increases by 24 ± 0.3%. But by doubling the diameter, the adsorption energy increased only by 9.8 ± 0.25%.     

Predictive simulations of the structural and adsorptive properties for PIM-1 variations

Despite the sizeable and growing body of research on polymers of intrinsic microporosity (PIMs), a greater understanding of the relationship between the monomer, polymer–polymer and polymer–gas interaction is of significant interest. Methane (CH₄), carbon dioxide (CO₂), oxygen (O₂) and nitrogen (N₂) adsorption isotherms at 20°C and up to 20 bar obtained from grand canonical Monte Carlo simulations are presented for PIM-1, PIM-1c, PIM-1n and PIM-1f. The new proposed structure, PIM-1f, is presented and characterised by geometric accessible surface area, pore size distribution, radial distribution function, X-ray scattering and gas adsorption isotherms. PIM-1f increased the geometric surface area when compared with PIM-1; however, the higher system density in combination with the lack of strong adsorption sites yielded the least effective adsorbent for the gases analysed in this study. The gas solubility and ideal solubility selectivity values are also presented and compared with available experimental data for all gases and several gas mixtures illustrating that PIM-1c is the most effective functionality studied for adsorbing these four gases. The conclusions made here are projected to facilitate the design of a material that combines the higher surface area of PIM-1f with the high adsorption capacity of PIM-1c, which will improve the performance of future PIMs.     

Editorial

Abstract

Grand canonical molecular dynamics (GCMD) simulations are used to study the adsorption and desorption of Lennard-Jones nitrogen in three slit pore junction models of microporous graphite. These networks consist of two narrow pores separated by a wider (cavity) pore. We report results for cases where the narrow pore has a width of only two or three molecular diameters. Using the GCMD technique, a novel freezing transition is observed which results in pore blocking in the narrow pores of the network, which are less than 1 nm wide. This freezing results from the adsorption energy barrier at the junction between the narrow and wider pores. This type of pore blocking could account for the apparent increase in pore volume with increasing temperature that has been experimentally observed in microporous graphite systems. For networks in which the narrower pores are somewhat larger, with a width of 1.28 nm, this pore blocking effect is much reduced, and adsorbate molecules enter and fill the central cavity. In such cases, however, desorption is incomplete, some residual adsorbate remaining in the central cavity even at the lowest pressures.     

Molecular dynamics study of core–shell structure from carbon nanotube and platinum nanowire

The interaction between the carbon nanotubes (CNTs) and platinum (Pt) nanowires (NWs) was investigated using forced field-based molecular dynamics (MD) simulations. Our results display that the Pt NW can induce the self-assembly of the CNTs to form a shell-core structure, this is because of the van der Waals interaction and the offset face-to-face π–π stacking interaction. The diameter of the CNT plays a major role in the formation of shell–core structure. Furthermore, the position of the CNT on the Pt NW also affects the formation of shell–core configuration, whereas the cross section of the NWs has a negligible effect on the fabrication process. Moreover, the interaction between multi-wall carbon nanotube and Pt nanowires was also discussed in detail, it is worth noting that the formation conformation of the CNT is also much more stable.