Grand Canonical Monte Research Articles

Occurrence of methane in organic pores with surrounding free water: A molecular simulation study

Free water contained in shale reservoirs can influence the enrichment and transportation of shale gas. To accurately assess shale gas adsorption in shale reservoirs and improve recovery, it is crucial to understand the occurrence of gas and water. In this study, the occurrence of methane occupying the organic pores surrounded by free water is investigated using Grand Canonical Monte Carlo/Molecular Dynamics simulations, considering the effects of pressure, temperature and pore size. The center of the model represents methane adsorbed/free within the organic pores, while the regions on either side depict free water. Although water does not significantly penetrate organic pores, pressure, temperature, and pore size have a notable impact on the wettability of water on organic surfaces, resulting in variations in the concave liquid surface morphology. This results in varying degrees of competitive adsorption of water and methane near the carbonyl group. At lower pressures, although the capillary pressure decreases sharply with increasing pore size, the improved water wettability increases the extent of its intrusion along the pore surface, thereby enhancing the competitive adsorption of methane and water. At higher pressures, capillary pressure acts as a resistance, preventing water from invading the organic pores in significant quantities. Due to the weak affinity of organic pores for water, the same phenomenon was observed even after increasing the pore size and temperature to improve water wettability. In addition, high temperatures can lead to more pronounced water intrusion. Finally, it is hypothesized that competitive adsorption of methane and water is more pronounced at shallower burial depths and slightly larger pore sizes. This result is expected to provide insights for the accurate evaluation of gas adsorption in water-bearing shales.

Separation of SO2 and NO2 with the Zeolite Membrane: Molecular Simulation Insights into the Advantageous NO2 Dimerization Effect.

NO2 and SO2, as valuable chemical feedstock, are worth being recycled from flue gases. The separation of NO2 and SO2 is a key process step to enable practical deployment. This work proposes SO2 separation from NO2 using chabazite zeolite (SSZ-13) membranes and provides insights into the feasibility and advantages of this process using molecular simulation. Grand canonical ensemble Monte Carlo and equilibrium molecular dynamics methods were respectively adopted to simulate the adsorption equilibria and diffusion of SO2, NO2, and N2O4 on SSZ-13 at varying Si/Al (1, 5, 11, 71, +∞), temperatures (248-348 K), and pressures (0-100 kPa). The adsorption capacity and affinity (SO2 > N2O4 > NO2) demonstrated strong competitive adsorption of SO2 based on dual-site interactions and significant reduction in NO2 adsorption due to dimerization in the ternary gas mixture. The simulated order of diffusivity (NO2 > SO2 > N2O4) on SSZ-13 demonstrated rapid transport of NO2, strong temperature dependence of SO2 diffusion, and the impermeability of SSZ-13 to N2O4. The membrane permeability of each component was simulated, rendering a SO2/NO2 membrane separation factor of 26.34 which is much higher than adsorption equilibrium (6.9) and kinetic (2.2) counterparts. The key role of NO2-N2O4 dimerization in molecular sieving of SO2 from NO2 was addressed, providing a facile membrane separation strategy at room temperature.

Development of the ReaxFF Reactive Force-Field Description of Gold Oxides

For the investigation of the interaction between oxygen and gold over length- and time-scales which reflect the operation of real catalysts, the reactive force-field (ReaxFF) description of the O/Au interaction has been developed. This development has been achieved in two stages: first, by fitting the parameters of the potential against an extensive set of both bulk and surface Au, O2, and gold oxides derived from full quantum mechanical simulations. The resulting potential has been used in a series of molecular dynamics (MD) simulations emulating the interaction between oxygen and the Au(111), the missing-row (1 × 2)-mr-Au(110), pairing-row (1 × 3)-pr-Au(110), trenched (1 × 3)-tr-Au(110), and added-row (2 × 1)-ar-Au(100) surfaces. These simulations have shown, in agreement with experimental studies, that oxygen diffusion from the surface to the bulk is heavily limited and generally only possible when thermal processing has started melting the Au substrate. Grand canonical Monte Carlo/molecular dynamics (...

Critical temperature estimation of bulk and confined atomic fluid using vapour−liquid interfacial free energy

The critical temperatures of bulk and confined atomic fluids are investigated using values of the vapour−liquid interfacial free energy of coexistence obtained from grand-canonical transition-matrix Monte Carlo simulations using a histogram reweighting technique. The temperature corresponding to zero interfacial free energy of coexistence is the estimated critical temperature for the system under investigation. Slit width of confined atomic fluid for this investigation is varied from 40 to 1 fluid particle diameter. The obtained critical temperatures have shown nonlinear monotonic trend with inverse of slit width. Moreover, five different linear regimes of critical temperature are observed in the studied range of slit width. Interestingly, in the slit width range of less than two fluid particle diameters, the critical temperature approaches two-dimensional value and remains approximately indifferent with a decrease in slit width up to one fluid particle diameter. This investigation also reveals that the critical temperature of bulk and confined atomic fluid estimated using the vapour−liquid interfacial free energy of coexistence is within reasonable accuracy with that obtained using the simplified form of scaling law.

Optimised Mie potentials for phase equilibria: application to alkynes

ABSTRACTA transferable united-atom force field, based on Mie potentials, is presented for alkynes. The performance of the optimised Mie potential parameters is assessed for 1-alkynes and 2-alkynes using grand canonical histogram-reweighting Monte Carlo simulations. For each compound, vapour–liquid coexistence curves, vapour pressures, heats of vapourisation, critical properties and normal boiling points are predicted and compared to experiment. Experimental saturated liquid densities are reproduced to within 2% average absolute deviation (AAD), except for 1-hexyne, which are reproduced with 3% AAD. Experimental saturated vapour pressures are reproduced to within 3% AAD, except for 1-pentyne, 2-pentyne and 2-hexyne, where deviations from experiment of up to 20% AAD were observed. Binary phase diagrams, predicted from Gibbs ensemble Monte Carlo simulations, for propane + propyne, propene + propyne and propadiene + propyne, are in close agreement with experiment.

Effect of surface-screening parameter of the Yukawa potential model on vapour–liquid phase coexistence and critical-point properties of confined Yukawa fluid

We report the effect of surface-screening parameter of Yukawa potential model on vapour–liquid phase coexistence and critical-point properties of slit–pore-confined Yukawa fluid, using grand canonical transition-matrix Monte Carlo along with the histogram reweighting method. The effect of surface-screening parameter on the vapour–phase coexistence density is insignificant for the studied system. On the other hand, significant effect of surface-screening parameter is observed on liquid phase coexistence density. With increasing surface-screening parameter, liquid phase coexistence density decreases. Critical-point properties have shown monotonic decreasing trends with increase in surface-screening parameter. Moreover, the effect of change of surface-screening parameter is least on critical temperature changes as compared to critical density and critical pressure changes for the studied Yukawa system in this work.

Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors.

Occluded ligand-binding pockets (LBP) such as those found in nuclear receptors (NR) and G-protein coupled receptors (GPCR) represent a significant opportunity and challenge for computer-aided drug design. To determine free energies maps of functional groups of these LBPs, a Grand-Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) strategy is combined with the Site Identification by Ligand Competitive Saturation (SILCS) methodology. SILCS-GCMC/MD is shown to map functional group affinity patterns that recapitulate locations of functional groups across diverse classes of ligands in the LBPs of the androgen (AR) and peroxisome proliferator-activated-γ (PPARγ) NRs and the metabotropic glutamate (mGluR) and β2-adreneric (β2AR) GPCRs. Inclusion of protein flexibility identifies regions of the binding pockets not accessible in crystal conformations and allows for better quantitative estimates of relative ligand binding affinities in all the proteins tested. Differences in functional group requirements of the active and inactive states of the β2AR LBP were used in virtual screening to identify high efficacy agonists targeting β2AR in Airway Smooth Muscle (ASM) cells. Seven of the 15 selected ligands were found to effect ASM relaxation representing a 46% hit rate. Hence, the method will be of use for the rational design of ligands in the context of chemical biology and the development of therapeutic agents.

Anisotropic diffusion of hydrogen in nanoporous carbons

It is accepted that hydrogen transport capacity through carbons depends on the anisotropy of the empty spaces that constitute their porous structure. However, very little is known about this relationship. Computational simulation is an excellent tool to accomplish this kind of studies. Simulation requires digital representations of materials and a model describing the interaction potential among the gas molecules and the solids surfaces. In this work, it is proposed to use the analytical solutions of the truncated pore problem for modeling the potentials, and an immiscible lattice gas for obtaining the representations. The degree of anisotropy was quantified by using the mean intercept length method. The adsorption isotherms and the self-diffusion coefficients in the three orthogonal directions were found by the grand canonical and kinetic Monte Carlo methods, respectively. The results suggest the existence of a gas pressure at which a molecular saturation threshold (Ps) is reached. Ps determines if the degree of anisotropy is or not a representative variable of diffusive transport. For P ≤ Ps, the degree of anisotropy favors the molecular mobility. When P > Ps, the degree of anisotropy loses influence on mobility.

Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials.

We developed a novel scheme based on the grand-canonical Monte Carlo/Brownian dynamics simulations and have extended it to studies of ion currents across three nanopores with the potential for single-stranded DNA (ssDNA) sequencing: solid-state nanopore Si₃N₄, α-hemolysin, and E111N/M113Y/K147N mutant. To describe nucleotide-specific ion dynamics compatible with ssDNA coarse-grained model, we used the inverse Monte Carlo protocol, which maps the relevant ion-nucleotide distribution functions from all-atom molecular dynamics (MD) simulations. Combined with the previously developed simulation platform for Brownian dynamics simulations of ion transport, it allows for microsecond- and millisecond-long simulations of ssDNA dynamics in the nanopore with a conductance computation accuracy that equals or exceeds that of all-atom MD simulations. In spite of the simplifications, the protocol produces results that agree with the results of previous studies on ion conductance across open channels and provide direct correlations with experimentally measured blockade currents and ion conductances that have been estimated from all-atom MD simulations.

Influences of lithium doping and fullerene impregnation on hydrogen storage in metal organic frameworks

Using the grand canonical ensemble Monte Carlo method, two similar metal organic frameworks (isoreticular MOFs [IRMOF]-12 and -14) and their modified structures by doping lithium (Li) atoms above the organic units and/or impregnating with fullerenes in their cavities have been employed to investigate the capacities of H2 storage. Our simulations show that the H2 uptakes of Li-C60@Li-IRMOF-12 and Li-C60@Li-IRMOF-14 achieve the U.S. Department of Energy targets before 2017 both in gravimetric density and in volumetric density at 243 K and 100 bar. Combining the results of IRMOF-10-based structures, we further study the relationships between the H2 uptakes and the physical properties of the materials to identify the influence factors on the H2 storage at room temperature.

A comparative study of critical temperature estimation of atomic fluid and chain molecules using fourth-order Binder cumulant and simplified scaling laws

Grand-canonical transition-matrix Monte Carlo simulation with histogram reweighting and finite-size scaling technique are used to calculate fourth-order Binder cumulant of order parameter along the vapour–liquid coexistence line to calculate the critical temperature of bulk and confined square-well fluid in slit pore of two pore sizes. Further, this approach is utilised to estimate the critical temperatures of relatively more complex fluids such as n-alkanes confined in graphite and mica slit pores of different slit widths. The estimated critical temperatures are compared with the critical temperature obtained for the same systems using simplified form of the scaling law. This investigation reveals that critical temperatures of simple and complex fluids in bulk state and under confinement, estimated using the scaling law, are within reasonable accuracy with that obtained using more accurate and rigorous approach of fourth-order Binder's cumulant.

Modeling, Ion Conductance, and Electrostatic Properties of the Protective Antigen Pore Structure of Anthrax Toxin

Despite repeated efforts, an atomic-resolution structure of the anthrax toxin protective antigen (PA) in its membrane-embedded pore form remains elusive. Recently, we determined the structure of the PA-pore at 16.0 A resolution using cryo-electron microscopy (cryo-EM) which signified progress but remained short of the desired atomic resolution. In this work, we employed a computational prediction approach and constructed the model structure of the heptameric PA-pore using I-TASSER complemented by the TACOS force field. Importantly, the electron density map obtained from the cryo-EM was used as an additional restraint during the modeling process. The overall structure was mushroom-shaped with a broad “cap” region and a narrow elongated “stem” in the form of a β-barrel. Remarkably, the β-barrel was not a straight cylinder, but “cigar-shaped” with a prominent bulge followed by a constriction region. The Poisson-Boltzmann electrostatic potential revealed that the structure featured rings of positively charged patches followed by negatively charged patches which can be potentially used to explain the proposed Brownian-ratchet mechanism of protein translocation at the PA-pore. A number of low-resolution structural features obtained previously from mutagenesis studies were used to initially corroborate the validity of the structure. Finally, grand-canonical Monte Carlo/Brownian dynamics simulations were conducted to calculate the ion conductance (KCl) and selectivity across the pore, which were found to be remarkably close to the experimental measurements and far better than those from previous modeling attempts of the PA-pore structure.

Surface phase transitions of multiple-site associating fluids

Surface phase transitions of Lennard–Jones (LJ) based two- and four-site associating fluids have been studied for various associating strengths using grand-canonical transition matrix Monte Carlo simulations. Our results suggest that, in the case of a smooth surface, represented by a LJ 9-3-type potential, multiple-site associating fluids display a prewetting transition within a certain temperature range. However, the range of the prewetting transition decreases with increasing associating strength and increasing number of sites on the fluid molecules. With the addition of associating sites on the surface, a quasi-2D vapor–liquid transition may appear, which is observed at a higher surface site density for weaker associating fluids. The prewetting transition at lower associating strength is found to shift towards the quasi-2D vapor–liquid transition with increasing surface site density. However, for highly associating fluids, the prewetting transition is still intact, but shifts slightly towards the lower temperature range. Adsorption isotherms, chemical potentials and density profiles are used to characterize surface phase transitions.

Optimaization of Single-Walled Carbon Nanotube for Adsorption of Methane

In this paper, methane adsorption in single-walled carbon nanotube (SWNT) has been simulated by using the grand canonical ensemble Monte Carlo (GCMC) method. Lennard-Jones (LJ) potential is used to represent the fluid-fluid interaction, Lennard-Jones potential and integral method are used to calculation of the potential between fluid molecules and carbon atoms, respectively. In the simulation, two methods of calculation of potential between fluid molecules and SWNT are compared. The potential calculated by the two methods are almost the same. Then the influence of diameter of SWNT on the usable capacity ratio (UCR) is analyzed, and the parameters of the SWNT which has the best adsorption performance at 300K is recommended under certain pressure.

Computational Simulation of Methane Adsorption in Single-Walled Carbon Nanotube

In this paper, methane adsorption in single-walled carbon nanotube (SWNT) has been simulated by using the grand canonical ensemble Monte Carlo (GCMC) method. Lennard-Jones (LJ) potential is used to represent the fluid-fluid interaction, and integral method is used to calculation of the potential between fluid molecules and carbon atoms. In the simulation, adsorption isotherms of methane in the (15, 15), (20, 20), (25, 25) and (30, 30) SWNT are simulated.

CHARMM-GUI: Brining Advanced Computational Techniques to Web Interface

The CHARMM-GUI resource (www.charmm-gui.org) has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. We have made significant efforts to implement basic and common molecular dynamics simulation techniques into web interface and the web interface has generated a multitude of positive feedback from our users. In this work, we describe our latest efforts to bringing more advanced molecular modeling and simulation techniques to the web interface, such as ligand binding free energy calculation, grand canonical Monte Carlo/Brownian dynamics, glycan reader and builder, electron microscopy density map fitting, protein-protein docking, and NMR structure calculation.

STRINGENT VERIFICATION OF THIRD ORDER + SECOND ORDER PERTURBATION DENSITY FUNCTION THEORY: BASED ON SHORT-RANGE SQUARE WELL POTENTIAL

A recently proposed third order + second order perturbation density functional theory (DFT) approach is made self-contained by using a virial pressure from the Ornstein–Zernike integral equation theory as input to determine the numerical value of an associated physical parameter. An exacting examination is formulated by applying the self-contained perturbation DFT approach to a short-range square well fluid of low temperatures subject to various external fields and comparing the theoretical results for density profiles to the corresponding grand canonical ensemble Monte Carlo simulation results. The comparison seems favorable for the third order + second order perturbation DFT approach as a self-contained and accurate predictive approach. It is surprisingly found that this self-contained third order + second order perturbation DFT approach is displayed outstandingly even if a deep SW perturbation term is being accounted for by a second order perturbation expansion. A discussion is presented about potential opportunity for this perturbation scheme.

Vapour–liquid phase equilibria of simple fluids confined in patterned slit pores

We present the influence of surface heterogeneity on the vapour–liquid phase behaviour of square-well fluids in slit pores using grand-canonical transition-matrix Monte Carlo simulations along with the histogram-reweighting method. Properties such as phase coexistence envelopes, critical properties and local density profiles of the confined SW fluid are reported for chemically and physically patterned slit surfaces. It is observed that in the chemically patterned pores, fluid–fluid and surface attraction parameters along with the width of attractive and inert stripes play fundamentally different roles in the phase coexistence and critical properties. On the other hand, pillar gap and height significantly affect the vapour–liquid equilibria in the physically patterned slit pores. We also present the effect of chemically and physically patterned slit surfaces on the spreading pressure.

Ion Selectivity of α-Hemolysin with β-Cyclodextrin Adapter. II. Multi-Ion Effects Studied with Grand Canonical Monte Carlo/Brownian Dynamics Simulations

In a previous study of ion selectivity of alpha-hemolysin (alphaHL) in complex with beta-cyclodextrin (betaCD) adapter, we calculated the potential of mean force (PMF) and characterized the self-diffusion coefficients of isolated K(+) and Cl(-) ions using molecular dynamics simulations (Y. Luo et al., "Ion Selectivity of alpha-Hemolysin with beta-Cyclodextrin Adapter: I. Single Ion Potential of Mean Force and Diffusion Coefficient"). In the present effort, these results pertaining to single isolated ions in the wide aqueous pore are extended to take into account multi-ion effects. The grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) algorithm is used to simulate ion currents through the wild-type alphaHL ion channel, as well as two engineered alphaHL mutants, with and without the cyclic oligosaccaride betaCD lodged in the lumen of the pore. The GCMC/BD current-voltage curves agree well with experimental results and show that betaCD increases the anion selectivity of alphaHL. Comparisons between multi-ion PMFs from GCMC/BD simulations and single-ion PMFs demonstrate that multi-ion effects and pore shape are crucial for explaining this behavior. It is concluded that the narrow betaCD adapter increases the anion selectivity of alphaHL because it reduces the pore radius locally, which decreases the ionic screening and the dielectric shielding of the strong electrostatic field induced by a nearby ring of positively charged alphaHL side chains.

Surface tension and vapour–liquid phase coexistence of variable-range hard-core attractive Yukawa fluids

The vapour–liquid phase coexistence and surface tension of hard-core Yukawa fluids with short attraction range, λ = 8.0, 9.0 and 10.0, are reported using grand-canonical transition-matrix Monte Carlo (GC-TMMC) with the histogram reweighting method. Surface tension is calculated using finite-size scaling approach of Binder. We also compare GC-TMMC results with the available literature data for Yukawa fluids with λ = 1.8, 3.0 and 4.0. Critical properties obtained from rectilinear diameter approach and least square-technique are also reported. GC-TMMC results are found to be more precise than the previous reported values. We also present the corresponding state of surface tension for extremely short-range attractive Yukawa fluids.