Molecular Dynamics Simulation of Sorption of Gases in Polystyrene

Self-Assembly of Model Three- and Four-Patch Colloidal Particles in Two Dimensions

A coarse-grained effective solvent model of two-patch particles is extended to study the self-assembly of three- and four-patch particles to two-dimensional honeycomb and square lattices, respectively. Employing this model, grand canonical ensemble simulations are done to calculate vapor-liquid equilibria and the critical temperatures for patchy particles of various patch widths. The range of stability of the liquid, although very limited compared to isotropic particles, which interact through a longer-range potential, depends on the patch width and on the number of patches. Biased sampling and unbiased simulations are also done to investigate the mechanism of nucleation and crystal growth for honeycomb and square lattices, self-assembled from three- and four-patch particles, respectively. A two-step mechanism governs the nucleation of both lattices. In the first step, the particles form a dense amorphous network, and in the second step, the particles inside the amorphous network reorient to form crystalline nuclei. Barrier heights for the nucleation of honeycomb and square lattices are 7.8 kBT and 7.4 kBT, which are close to the reported values for the nucleation of the kagome lattice. In agreement with confocal microscopy experiments, the self-assembly in a honeycomb lattice involves the formation of 5- to 7-membered rings. The 5- and 7-membered rings hamper the nucleation of the honeycomb lattice, through defect formation and rotation of the symmetry planes of crystals that form at their surfaces. With the progress of self-assembly, a substantial amount of restructuring of the defects and crystals in their vicinity is needed to heal the defects.

Molecular Structure and Dynamics in Wet Gecko β-Keratin

Molecular dynamics simulations are performed to investigate the molecular picture of water sorption in gecko keratin and the influence of relative humidity (RH) on the local structure and dynamics in water-swollen keratin. At low RHs, water sorption occurs through hydrogen bonding of water with the hydrophilic groups of keratin. At high RHs (>80%), additional water molecules connect to the first "layer" of amide-connected water molecules (multimolecular sorption) through hydrogen bonds, giving rise to a sigmoidal shape of the sorption isotherm. This causes the formation of large chain-like clusters surrounding the hydrophilic groups of keratin, which upon a further increase of the RH form a percolating water network. An examination of the dynamics of water molecules sorbed in keratin demonstrates that there are two states, bound and free, for water. The dynamics of water in these states depends on the RH. At low RHs, large-scale translational motions of tightly bound water molecules to keratin are needed to remake the entire hydration shell of the keratin. At high RHs (>80%), the water molecules more quickly exchange between the two states. The center-of-mass mean-square displacement of water molecules indicates a hopping motion of water molecules in the keratin solvation shell. The hopping mechanism is more pronounced at RHs < 80%. At higher RHs, water translation through water clusters (water network) dominates. We have observed two regimes for the dependence of dynamical properties on the RH: a regime of gradual increase of the dynamics over 10% < RH < 80% and a regime of drastic dynamic acceleration at RH > 80%. The latter regime begins exactly where the water uptake and the volume swelling also increase much more and where a drastic change in the elastic properties of gecko keratin has been observed. A nearly linear relation between the relaxation times for all dynamical processes and the water content of gecko keratin is observed.

Permeation Characteristics of CH4 in PVDF with Crude Oil-Containing

The liner of reinforced thermoplastic composite pipes (RTPs) used for oil and gas gathering and transportation experienced blister failure due to gas permeation. Few reports have appeared on the problem of gas permeation in thermoplastics with absorbed crude oil. Accordingly, the permeability of CH₄ in polyvinylidene fluoride (PVDF) containing crude oil was studied at the normal service conditions by molecular simulations. The results showed that the solubility coefficients of CH₄ in PVDF containing crude oil were much lower than those in pure PVDF. It can be concluded that the crude oil molecules absorbed into PVDF occupied certain adsorption sites, resulting in a decrease in the adsorption capacity of CH₄ molecules in PVDF. The diffusion coefficients of CH₄ in oil-containing PVDF were significantly greater than in PVDF. This is because the absorption of oil molecules leads to the volume swelling of PVDF and then increases the free volume for diffusion. The permeation process showed that CH₄ molecules were selective-aggregate adsorbed in the region with low potential energy in oil-containing PVDF firstly, and then they vibrated within the holes of PVDF containing oil in most cases and jumped into the neighboring holes at high temperatures and pressures.

Self-Assembly of Model Triblock Janus Colloidal Particles in Two Dimensions

A simplified two-dimensional effective-solvent model of triblock Janus particles, consisting of three interaction sites in a linear configuration, a core particle, and two particles modeling the attractive patches at the poles, is developed to study the mechanism of nucleation and self-assembly in triblock Janus particles. The potential energy parameters are tuned against phase transition temperatures and free energy barriers to the nucleation of crystalline phases, calculated from our previous detailed model of Janus particles. Vapor-liquid equilibria and critical temperatures are calculated by grand-canonical molecular dynamics simulations for particles of different patch widths. With metadynamics, phase equilibria, mechanism of nucleation, and free energy barriers to nucleation are investigated. The minimum free energy path to nucleation indicates two steps. The first step, with a higher free energy increase, consists of the densification of the fluid into a disordered cluster. In the second step, of a lower free energy barrier, the inner particles of the disordered cluster reorient to form a crystalline nucleus. This two-step mechanism of nucleation of a kagome lattice is in complete agreement with the experiment and with our previous simulations using a detailed model of Janus particles. Large systems at a slight supersaturation generate multiple crystalline domains, which are misaligned at the grain boundaries. In complete agreement with the experiment and with previous simulation results, we observe a two-step mechanism for crystal growth: melting of the smaller (less stable) crystallites to a fluid followed by recrystallization at the surface of neighboring bigger (more stable) crystallites. A comparison of the present softer modeling of a Janus particle with harder models in the literature for self-assembly of Janus particles indicates that softer potentials stabilize open lattices (e.g., kagome) more than dense lattices (e.g., hexagonal). Also, experimental locations of phase transition points and barrier heights to nucleation are better reproduced by the present model than by the existing simple models.

Evaluation of Adsorption and Permeation Behaviors in Hydrated Nafion Membranes with Degradation

In the operation of proton exchange membrane fuel cells, its ionomeric-polymer membrane is easily attacked by free radicals, resulting in the degradation of performance. In this work, the chemical degradation effect of hydrated Nafion membranes on gas adsorption, diffusion, and permeation behaviors is evaluated by molecular dynamics and Monte Carlo simulation. The correlation of pore ratio, free volume, hydrophilic/hydrophobic interface as well as the connectivity of the hydrophilic domain of Nafion membranes with gas transport characteristics are revealed. The results demonstrate that large free volume, high large pore ratio, smooth hydrophilic/hydrophobic interface, and good connectivity of the hydrophilic domain are favorable for adsorption, diffusion, and permeability processes. The C-S bond and C-O-C bond attack of membranes can increase the gas adsorption amount, which becomes weak after the tertiary carbon is attacked.

The structure of CO2 and CH4 at the interface of a poly(urethane urea) oligomer model from the microscopic point of view

The world desperately needs new technologies and solutions for gas capture and separation. To make this possible, molecular modeling is applied here to investigate the structural, thermodynamic, and dynamical properties of a model for the poly(urethane urea) (PUU) oligomer model to selectively capture CO₂ in the presence of CH₄. In this work, we applied a well-known approach to derive atomic partial charges for atoms in a polymer chain based on self-consistent sampling using quantum chemistry and stochastic dynamics. The interactions of the gases with the PUU model were studied in a pure gas based system as well as in a gas mixture. A detailed structure characterization revealed high interaction of CO₂ molecules with the hard segments of the PUU. Therefore, the structural and energy properties explain the reasons for the greater CO₂ sorption than CH₄. We find that the CO₂ sorption is higher than the CH₄ with a selectivity of 7.5 at 298 K for the gas mixture. We characterized the Gibbs dividing surface for each system, and the CO₂ is confined for a long time at the gas-oligomer model interface. The simulated oligomer model showed performance above the 2008 Robeson's upper bound and may be a potential material for CO₂/CH₄ separation. Further computational and experimental studies are needed to evaluate the material.

Atomistic Investigation of Material Deformation Behavior of Polystyrene in Nanoimprint Lithography

This research investigates deformation behavior of polystyrene (PS) as a thermoplastic resist material for the thermal nanoimprint lithography (T-NIL) process. Molecular dynamics modeling was conducted on a PS substrate with dimensions 58 × 65 × 61 Å that was imprinted with a rigid, spherical indenter. The effect of indenter size, force, and imprinting duration were evaluated in terms of indentation depth, penetration depth, recovery depth, and recovery percentage of the polymer. The results show that the largest indenter, regardless of force, has the most significant impact on deformation behavior. The 40 Å indenter with a 1 µN of force caused the surface molecules to descend to the lowest point compared to the other indenters. An increase in indenter size resulted in higher penetration depth, recovery depth, and recovery percentage. Higher durations of imprint cycle (400 fs) resulted in plastic deformation of the PS material with minimal recovery (4 Å). The results of this research lay the foundation for explaining the effect of several T-NIL process parameters on virgin PS thermoplastic resist material.

How Alcoholic Disinfectants Affect Coronavirus Model Membranes: Membrane Fluidity, Permeability, and Disintegration

Atomistic molecular dynamics simulations have been carried out with a view to investigating the stability of the SARS-CoV-2 exterior membrane with respect to two common disinfectants, namely, aqueous solutions of ethanol and n-propanol. We used dipalmitoylphosphatidylcholine (DPPC) as a model membrane material and did simulations on both gel and liquid crystalline phases of membrane surrounded by aqueous solutions of varying alcohol concentrations (up to 17.5 mol %). While a moderate effect of alcohol on the gel phase of membrane is observed, its liquid crystalline phase is shown to be influenced dramatically by either alcohol. Our results show that aqueous solutions of only 5 and 10 mol % alcohol already have significant weakening effects on the membrane. The effects of n-propanol are always stronger than those of ethanol. The membrane changes its structure, when exposed to disinfectant solutions; uptake of alcohol causes it to swell laterally but to shrink vertically. At the same time, the orientational order of lipid tails decreases significantly. Metadynamics and grand-canonical ensemble simulations were done to calculate the free-energy profiles for permeation of alcohol and alcohol/water solubility in the DPPC. We found that the free-energy barrier to permeation of the DPPC liquid crystalline phase by all permeants is significantly lowered by alcohol uptake. At a disinfectant concentration of 10 mol %, it becomes insignificant enough to allow almost free passage of the disinfectant to the inside of the virus to cause damage there. It should be noted that the disinfectant also causes the barrier for water permeation to drop. Furthermore, the shrinking of the membrane thickness shortens the gap needed to be crossed by penetrants from outside the virus into its core. The lateral swelling also increases the average distance between head groups, which is a secondary barrier to membrane penetration, and hence further increases the penetration by disinfectants. At alcohol concentrations in the disinfectant solution above 15 mol %, we reliably observe disintegration of the DPPC membrane in its liquid crystalline phase.

Molecular Simulations and Mechanistic Analysis of the Effect of CO2 Sorption on Thermodynamics, Structure, and Local Dynamics of Molten Atactic Polystyrene

A simulation strategy encompassing different scales was applied to the systematic study of the effects of CO₂ uptake on the properties of atactic polystyrene (aPS) melts. The analysis accounted for the influence of temperature between 450 and 550 K, polymer molecular weights (M _w) between 2100 and 31000 g/mol, and CO₂ pressures up to 20 MPa on the volumetric, swelling, structural, and dynamic properties of the polymer as well as on the CO₂ solubility and diffusivity by performing molecular dynamics (MD) simulations of the system in a fully atomistic representation. A hierarchical scheme was used for the generation of the higher M _w polymer systems, which consisted of equilibration at a coarse-grained level of representation through efficient connectivity-altering Monte Carlo simulations, and reverse-mapping back to the atomistic representation, obtaining the configurations used for subsequent MD simulations. Sorption isotherms and associated swelling effects were determined by using an iterative procedure that incorporated a series of MD simulations in the NPT ensemble and the Widom test particle insertion method, while CO₂ diffusion coefficients were extracted from long MD runs in the NVE ensemble. Solubility and diffusivity compared favorably with experimental results and with predictions of the Sanchez-Lacombe equation of state, which was reparametrized to capture the M _w dependence of polymer properties with greater accuracy. Structural features of the polymer matrix were correctly reproduced by the simulations, and the effects of gas concentration and M _w on structure and local dynamics were thoroughly investigated. In the presence of CO₂, a significant acceleration of the segmental dynamics of the polymer occurred, more pronouncedly at low M _w. The speed-up effect caused by the swelling agent was not limited to the chain ends but affected the whole chain in a similar fashion.

Molecular simulation as a computational pharmaceutics tool to predict drug solubility, solubilization processes and partitioning

In this review we will discuss how computational methods, and in particular classical molecular dynamics simulations, can be used to calculate solubility of pharmaceutically relevant molecules and systems. To the extent possible, we focus on the non-technical details of these calculations, and try to show also the added value of a more thorough and detailed understanding of the solubilization process obtained by using computational simulations. Although the main focus is on classical molecular dynamics simulations, we also provide the reader with some insights into other computational techniques, such as the COSMO-method, and also discuss Flory-Huggins theory and solubility parameters. We hope that this review will serve as a valuable starting point for any pharmaceutical researcher, who has not yet fully explored the possibilities offered by computational approaches to solubility calculations.

Size-dependent penetrant diffusion in polymer glasses

Molecular Dynamics simulations are used to understand the underpinning basis of the transport of gas-like solutes in deeply quenched polymeric glasses. As found in previous work, small solutes, with sizes smaller than 0.15 times the chain monomer size, move as might be expected in a medium with large pores. In contrast, the motion of larger solutes is activated and is strongly facilitated by matrix motion. In particular, solute motion is coupled to the local elastic fluctuations of the matrix as characterized by the Debye-Waller factor. While similar ideas have been previously proposed for the viscosity of supercooled liquids above their glass transition, to our knowledge, this is the first illustration of this concept in the context of solute mass transport in deeply quenched polymer glasses.

Transport Diffusion of Light Gases in Polyethylene Using Atomistic Simulations

We explore the temperature dependence of the self-, corrected-, and transport-diffusivities of CO₂, CH₄, and N₂ in a polyethylene (PE) polymer membrane through equilibrium molecular dynamics simulations. We also investigate the morphology of the polymer membrane based on the intermolecular radial distribution function, free volume, and pore size distribution analysis. The results indicate the existence of 1.5-3 Å diameter pores in the PE membrane, and with the increase in the temperature, the polymer swells linearly with changing slope at 450 K in the absence of gas and exponentially in the presence of gas. The gas adsorption isotherms extracted via a two-step methodology, considering the dynamics and structural transitions in the polymer matrix upon gas adsorption, were fitted using a "two-mode sorption" model. Our results suggest that CO₂ adsorbs strongly, whereas N₂ shows weak adsorption in PE. The results demonstrate that CO₂ is more soluble, whereas N₂ is least soluble. Further, it is found that an increase in the temperature negatively impacts the solubility of CO₂ and CH₄ but positively for N₂; this reverse solubility behavior is due to increased availability of pores accessible to N₂, which are kinetically closed at the lowest temperatures. The reported self-diffusivities of the gases from our simulations are on the order of 10^-6 cm²/s, consistent with the experimental evidence, whereas transport-diffusivities are 2 orders of magnitude higher than self-diffusivities. Furthermore, the temperature dependence of the self-diffusivity follows Arrhenius behavior, whereas the transport-diffusivity follows non-Arrhenius behavior having different activation energies in low and high temperature regions. Also, it is seen that loading has little effect on the self- and corrected-diffusion coefficients of all gases in the PE membrane.

Solubility of Carbon Dioxide in Pentaerythritol Hexanoate: Molecular Dynamics Simulation of a Refrigerant-Lubricant Oil System

We have investigated the solubility and the solvation structure between a refrigerant (carbon dioxide, CO2) and a lubricant oil (pentaerythritol hexanoate, PEC6) by molecular dynamics simulations. First, to investigate the solubility, we calculated the vapor-liquid equilibrium pressure. The chemical potential of the liquid phase and the gas phase were calculated, and the equilibrium state was obtained from the crossing point of these chemical potentials. The equilibrium pressures agreed well with experimental data over a wide range of temperatures and mole fractions of CO2. Second, the solvation structure was also investigated on a molecular scale. We found the following characteristics. First, the tails of the lubricant oil are relatively rigid inside the ester groups but flexible beyond. Second, CO2 molecules barely enter the lubricant core as delimited by the ester groups. Third, the double-bonded oxygen atoms of the ester groups are good sorption sites for CO2. Fourth, only a few CO2 molecules are attached to more than one carbonyl oxygen simultaneously. Finally, there is also significant unspecific sorption of CO2 in the alkane tail region. These results indicate that increasing the size of the rigid lubricant core would probably decrease the solubility, whereas increasing the number of polar groups would increase it.

Sorption and diffusion of carbon dioxide and nitrogen in poly(methyl methacrylate)

Molecular dynamics simulations are performed to determine the solubility and diffusion coefficient of carbon dioxide and nitrogen in poly(methyl methacrylate) (PMMA). The solubilities of CO2 in the polymer are calculated employing our grand canonical ensemble simulation method, fixing the target excess chemical potential of CO2 in the polymer and varying the number of CO2 molecules in the polymer matrix till establishing equilibrium. It is shown that the calculated sorption isotherms of CO2 in PMMA, employing this method well agrees with experiment. Our results on the diffusion coefficients of CO2 and N2 in PMMA are shown to obey a common hopping mechanism. It is shown that the higher solubility of CO2 than that of N2 is a consequence of more attractive interactions between the carbonyl group of polymer and the sorbent. While the residence time of CO2 beside the carbonyl group of polymer is about three times higher than that of N2, the diffusion coefficient of CO2 in PMMA is higher than that of N2. The higher diffusion coefficient of CO2, compared to N2, in PMMA is shown to be due to the higher (≈3 times) swelling of polymer upon CO2 uptake.

Pure and Modified Co-Poly(amide-12-b-ethylene oxide) Membranes for Gas Separation Studied by Molecular Investigations

This paper deals with a theoretical investigation of gas transport properties in a pure and modified PEBAX block copolymer membrane with N-ethyl-o/p-toluene sulfonamide (KET) as additive molecules. Molecular dynamics simulations using COMPASS force field, Gusev-Suter Transition State Theory (TST) and Monte Carlo methods were used. Bulk models of PEBAX and PEBAX/KET in different copolymer/additive compositions were assembled and analyzed to evaluate gas permeability and morphology to characterize structure-performance relationships.

Grand canonical ensemble molecular dynamics simulation of water solubility in polyamide-6,6

Grand canonical ensemble molecular dynamics simulation is employed to calculate the solubility of water in polyamide-6,6. It is shown that performing two separate simulations, one in the polymeric phase and one in the gaseous phase, is sufficient to find the phase coexistence point. In this method, the chemical potential of water in the polymer phase is expanded as a first-order Taylor series in terms of pressure. Knowing the chemical potential of water in the polymer phase in terms of pressure, another simulation for water in the gaseous phase, in the grand canonical ensemble, is done in which the target chemical potential is set in terms of pressure in the gas phase. The phase coexistence point can easily be calculated from the results of these two independent simulations. Our calculated sorption isotherms and solubility coefficients of water in polyamide-6,6, over a wide range of temperatures and pressures, agree with experimental data.