Boltzmann bias grand canonical Monte Carlo

We derive an efficient method for the insertion of structured particles in grand canonical Monte Carlo simulations of adsorption in very confining geometries. We extend this method to path integral simulations and use it to calculate the isotherm of adsorption of hydrogen isotopes in narrow carbon nanotubes (two-dimensional confinement) and slit pores (one-dimensional confinement) at the temperatures of 20 and 77 K, discussing its efficiency by comparison to the standard path integral grand canonical Monte Carlo algorithm. We use this algorithm to perform multicomponent simulations in order to calculate the hydrogen isotope selectivity for adsorption in narrow carbon nanotubes and slit pores at finite pressures. The algorithm described here can be applied to the study of adsorption of real oligomers and polymers in narrow pores and channels.     

Acceleration of Monte Carlo simulations through spatial updating in the grand canonical ensemble

A new grand canonical Monte Carlo algorithm for continuum fluid models is proposed. The method is based on a generalization of sequential Monte Carlo algorithms for lattice gas systems. The elementary moves, particle insertions and removals, are constructed by analogy with those of a lattice gas. The updating is implemented by selecting points in space (spatial updating) either at random or in a definitive order (sequential). The type of move, insertion or removal, is deduced based on the local environment of the selected points. Results on two-dimensional square-well fluids indicate that the sequential version of the proposed algorithm converges faster than standard grand canonical algorithms for continuum fluids. Due to the nature of the updating, additional reduction of simulation time may be achieved by parallel implementation through domain decomposition.     

Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations

The binding of a ligand to a receptor is often associated with the displacement of a number of bound water molecules. When the binding site is exposed to the bulk region, this process may be sampled adequately by standard unbiased molecular dynamics trajectories. However, when the binding site is deeply buried and the exchange of water molecules with the bulk region may be difficult to sample, the convergence and accuracy in free energy perturbation (FEP) calculations can be severely compromised. These problems are further compounded when a reduced system including only the region surrounding the binding site is simulated. To address these issues, we couple molecular dynamics (MD) with grand canonical Monte Carlo (GCMC) simulations to allow the number of water to fluctuate during an alchemical FEP calculation. The atoms in a spherical inner region around the binding pocket are treated explicitly while the influence of the outer region is approximated using the generalized solvent boundary potential (GSBP). At each step during thermodynamic integration, the number of water in the inner region is equilibrated with GCMC and energy data generated with MD is collected. Free energy calculations on camphor binding to a deeply buried pocket in cytochrome P450cam, which causes about seven water molecules to be expelled, are used to test the method. It concluded that solvation free energy calculations with the GCMC/MD method can greatly improve the accuracy of the computed binding free energy compared to simulations with fixed number of water.     

Pore size distribution analysis of selected hexagonal mesoporous silicas by grand canonical Monte Carlo simulations

We combine here a regularization procedure with individual adsorption isotherms obtained from grand canonical Monte Carlo simulations in order to obtain reliable pore size distributions. The methodology is applied to two hexagonal high-ordered silica materials: SBA-15 and PHTS, synthesized in our laboratory. Feasible pore size distributions are calculated through an adaptable procedure of deconvolution over the adsorption integral equation, with two necessary inputs: the experimental adsorption data and individual adsorption isotherms, assuming the validity of the independent pore model. The application of the deconvolution procedure implies an adequate grid size evaluation (i.e., numbers of pores and relative pressures to be considered for the inversion, or kernel size), the fulfillment of the discret Picard condition, and the appropriate choice of the regularization parameter (L-curve criteria). Assuming cylindrical geometry for both porous materials, the same set of individual adsorption isotherms generated from molecular simulations can be used to construct the kernel to obtain the PSD of SBA-15 and PHTS. The PSD robustness is measured imposing random errors over the experimental data. Excellent agreement is found between the calculated and the experimental global adsorption isotherms for both materials. Molecular simulations provide new insights into the studied systems, pointing out the need of high-resolution isotherms to describe the presence of complementary microporosity in these materials.     

Monte Carlo simulations of chains confined inside a cube

Self-avoiding walks (SAWs) and random-flight walks (RFWs) of various lengths embedded on a simple cubic lattice have been computer generated inside cubes of varying side. If B is the side of the confining cube, we define the reduced cube side size B₀ as B₀ = (B − 1)/<r²>^1/2, where <r²>^1/2 is the root-mean-square end-to-end distance of the non-confined chains. Dimensionless diagrams are then given of the Monte Carlo estimates for the dimensions, the entropy, and the compressibility parameter PV/(kT) of the confined chains as a function of B₀. The comparative behaviour of the confined SAWs and RFWs is established, scaling properties are examined, and the Monte Carlo estimates compared with theory when such theory is available.     

Computation of interfacial properties via grand canonical transition matrix Monte Carlo simulation

We examine two free-energy-based methods for studying the wetting properties of a fluid in contact with a solid substrate. Application of the first approach involves examination of the adsorption behavior of a fluid at a single substrate, while the second technique requires investigation of the properties of a system confined between two parallel substrates. Both of the techniques rely upon computation and analysis of the density dependence of a system's surface free energy and provide the contact angle and solid-vapor and solid-liquid interfacial tensions for substrate-fluid combinations within the partial wetting regime. Grand canonical transition matrix Monte Carlo simulation is used to obtain the required free-energy curves. The methods examined within this work are general and are applicable to a wide range of molecular systems. We probe the performance of the methods by computing the interfacial properties for two systems in which an atomistic fluid interacts with a fcc crystal. For both of the systems studied we find good agreement between our results and those obtained via the mechanical definition of the interfacial tension.     

Grand canonical Monte Carlo simulations of water in protein environments

The grand canonical simulation algorithm is considered as a general methodology to sample the configuration of water molecules confined within protein environments. First, the probability distribution of the number of water molecules and their configuration in a region of interest for biochemical simulations, such as the active site of a protein, is derived by considering a finite subvolume in open equilibrium with a large system serving as a bulk reservoir. It is shown that the influence of the bulk reservoir can be represented as a many-body potential of mean force acting on the atoms located inside the subvolume. The grand canonical Monte Carlo (GCMC) algorithm, augmented by a number of technical advances to increase the acceptance of insertion attempts, is implemented, and tested for simple systems. In particular, the method is illustrated in the case of a pure water box with periodic boundary conditions. In addition, finite spherical systems of pure water and containing a dialanine peptide, are simulated with GCMC while the influence of the surrounding infinite bulk is incorporated using the generalized solvent boundary potential [W. Im, S. Berneche, and B. Roux, J. Chem. Phys. 114, 2924 (2001)]. As a last illustration of water confined in the interior of a protein, the hydration of the central cavity of the KcsA potassium channel is simulated.     

Molecular organization in liquids consisting of anisometric molecules: Monte Carlo simulations and comparison with theories

Monte Carlo computer simulations of systems of rigid anisometric molecules with axial ratio x 3, 4 and 5 have been performed at densities comparable to those of the mesogenic groups in liquid crystalline materials. The agreement between computer experiments and Flory-Ronca-Irvine theory is quite good. In particular, the nematic-isotropic transition temperatures found in the simulations are within 20 K of those predicted by the theory in all cases examined with x 3 and 4, and only slightly higher when x 5. Furthermore, the orientational distributions of the molecular long axes with respect to the nematic director are always nearly coincident with those evaluated according to the FRI theory, provided that the order parameter is the same. However, the order parameters at the transition points are smaller than expected on the basis of the theory, and closer to experimental values. Calculations performed by changing the size of the simulated systems prove that the reported results are size independent, while size dependent results are obtained with smaller systems.     

Structure and adsorption of a hard-core multi-Yukawa fluid confined in a slitlike pore: grand canonical Monte Carlo simulation and density functional study

Because of the increasing interest in studying the phenomenon exhibited by charge-stabilized colloidal suspensions in confining geometry, we present a density functional theory (DFT) for a hard-core multi-Yukawa fluid. The excess Helmholtz free-energy functional is constructed by using the modified fundamental measure theory and Rosenfeld's perturbative method, in which the bulk direct correlation function is obtained from the first-order mean spherical approximation. To validate the established theory, grand canonical ensemble Monte Carlo (GCMC) simulations are carried out to determine the density profiles and surface excesses of multi-Yukawa fluid in a slitlike pore. Comparisons of the theoretical results with the GCMC data suggest that the present DFT gives very accurate density profiles and surface excesses of multi-Yukawa fluid in the slitlike pore as well as the radial distribution functions of the bulk fluid. Both the DFT and the GCMC simulations predict the depletion of the multi-Yukawa fluid near a nonattractive wall, while the mean-field theory fails to describe this depletion in some cases. Because the simple form of the direct correlation function is used, the present DFT is computationally as efficient as the mean-field theory, but reproduces the simulation data much better than the mean-field theory.     

Thermodynamics and partitioning of homopolymers into a slit-A grand canonical Monte Carlo simulation study

Grand canonical ensemble Monte Carlo simulation (GCMC) combined with the histogram reweighting technique was used to study the thermodynamic equilibrium of a homopolymer solution between a bulk and a slit pore. GCMC gives the partition coefficients that agree with those from canonical ensemble Monte Carlo simulations in a twin box, and it also gives results that are not accessible through the regular canonical ensemble simulation such as the osmotic pressure of the solution. In a bulk polymer solution, the calculated osmotic pressure agrees very well with the scaling theory predictions both for the athermal polymer solution and the theta solution. However, one cannot obtain the osmotic pressure of the confined solution in the same way since the osmotic pressure of the confined solution is anisotropic. The chemical potentials in GCMC simulations were found to differ by a translational term from the chemical potentials obtained from canonical ensemble Monte Carlo simulations with the chain insertion method. This confirms the equilibrium condition of a polymer solution partition between the bulk and a slit pore: the chemical potentials of the polymer chain including the translational term are equal at equilibrium. The histogram reweighting method enables us to obtain the partition coefficients in the whole range of concentrations based on a limited set of simulations. Those predicted bulk-pore partition coefficient data enable us to perform further theoretical analysis. Scaling predictions of the partition coefficient at different regimes were given and were confirmed by the simulation data.     

Adsorption of benzene and propene in zeolite MCM-22: a grand canonical Monte Carlo study

The GCMC (grand canonical Monte Carlo) simulation technique was used to predict the competition adsorption characteristics of benzene and propene in different pore systems of MCM-22. The nine-site model of benzene was used, which proved to be effective and efficient. The zeolite was divided into three adsorption sites following a simulated annealing method. It is found that benzene and propene have the same preferential adsorption site and a similar adsorption order in different sites. Moreover, the pure and mixture isotherms of the three sites are drawn. From the isotherms, we obtained a selectivity reversal of the mixture isotherms of benzene and propene in different sites. It is also noted that the competition adsorption in the three adsorption sites for the two adsorbates can fall into three successive steps and the adsorption order of propene in mixture in these three sites is S3→S1→S2. A new model is presented to predict the benzene and propene adsorption equilibrium in MCM-22. This approach yields better multicomponent equilibrium predictions than ideal adsorbed solution theory (IAST). Isotherms at different mole fraction of benzene in gas phase indicate an advantage to increase the feed radio of benzene and propene. Thus, this work is helpful for a better understanding of the adsorption mechanism of benzene and propene in MCM-22 and hence the relation of the catalytic properties of the zeolite to its structure.     

Spatial updating grand canonical Monte Carlo algorithms for fluid simulation: generalization to continuous potentials and parallel implementation

Spatial updating grand canonical Monte Carlo algorithms are generalizations of random and sequential updating algorithms for lattice systems to continuum fluid models. The elementary steps, insertions or removals, are constructed by generating points in space either at random (random updating) or in a prescribed order (sequential updating). These algorithms have previously been developed only for systems of impenetrable spheres for which no particle overlap occurs. In this work, spatial updating grand canonical algorithms are generalized to continuous, soft-core potentials to account for overlapping configurations. Results on two- and three-dimensional Lennard-Jones fluids indicate that spatial updating grand canonical algorithms, both random and sequential, converge faster than standard grand canonical algorithms. Spatial algorithms based on sequential updating not only exhibit the fastest convergence but also are ideal for parallel implementation due to the absence of strict detailed balance and the nature of the updating that minimizes interprocessor communication. Parallel simulation results for three-dimensional Lennard-Jones fluids show a substantial reduction of simulation time for systems of moderate and large size. The efficiency improvement by parallel processing through domain decomposition is always in addition to the efficiency improvement by sequential updating.     

Size-effects on simulations in the grand canonical ensemble

Results are presented for the effect of periodic boundary conditions on predictions made using the grand canonical ensemble for systems of limited size. A Monte Carlo study of a realistic gas-solid adsorption model and an exact study of the Tonks gas both show that it is necessary for the minor dimension of the replicated system to be 5 σ or greater if errors in the partition function equivalent to δμ > 0.2 kT are to be avoided. The heat capacity C_μ has similar requirements. However, for quantities such as the isosteric heat of adsorption, <N > and <U > even a dimension as small as 3σ does not lead to serious errors. An examination is presented of possible implications for studies of phase changes.     

Effect of surface functionalities on gas adsorption in microporous carbons: a grand canonical Monte Carlo study

In an attempt to offer a more realistic picture of adsorption in highly heterogeneous porous systems, such as oxygen functionalized porous carbons, we consider a series of carbon surfaces baring different amounts of oxygen functionalities (hydroxyl and epoxy). These surfaces are used to construct “oxidized” slit pores of varying width and functionality. With the aid of such inhomogeneous structures we study the interaction of Ar (87 K) inside “functionalized” pores and report grand canonical Monte Carlo adsorption simulations results. Based on our simulation data, we discuss the role of chemical heterogeneity on adsorbed/gas phase equilibrium properties such as density, heat of adsorption, and molecular packing within the pores. Comparisons are made with the case of the oxygen–free (completely homogeneous) slit pore models and conclusions on the suitability of Ar based pore size distributions for functionalized porous carbons are drawn.     

Storage of hydrogen at 303 K in graphite slitlike pores from grand canonical Monte Carlo simulation

Grand canonical Monte Carlo (GCMC) simulations were used for the modeling of the hydrogen adsorption in idealized graphite slitlike pores. In all simulations, quantum effects were included through the Feynman and Hibbs second-order effective potential. The simulated surface excess isotherms of hydrogen were used for the determination of the total hydrogen storage, density of hydrogen in graphite slitlike pores, distribution of pore sizes and volumes, enthalpy of adsorption per mole, total surface area, total pore volume, and average pore size of pitch-based activated carbon fibers. Combining experimental results with simulations reveals that the density of hydrogen in graphite slitlike pores at 303 K does not exceed 0.014 g/cm(3), that is, 21% of the liquid-hydrogen density at the triple point. The optimal pore size for the storage of hydrogen at 303 K in the considered pore geometry depends on the pressure of storage. For lower storage pressures, p < 30MPa, the optimal pore width is equal to a 2.2 collision diameter of hydrogen (i.e., 0.65 nm), whereas, for p congruent with 50MPa, the pore width is equal to an approximately 7.2 collision diameter of hydrogen (i.e., 2.13 nm). For the wider pores, that is, the pore width exceeds a 7.2 collision diameter of hydrogen, the surface excess of hydrogen adsorption is constant. The importance of quantum effects is recognized in narrow graphite slitlike pores in the whole range of the hydrogen pressure as well as in wider ones at high pressures of bulk hydrogen. The enthalpies of adsorption per mole for the considered carbonaceous materials are practically constant with hydrogen loading and vary within the narrow range q(st) congruent with 7.28-7.85 kJ/mol. Our systematic study of hydrogen adsorption at 303 K in graphite slitlike pores gives deep insight into the timely problem of hydrogen storage as the most promising source of clean energy. The calculated maximum storage of hydrogen is equal to approximately 1.4 wt %, which is far from the United States Department of Energy (DOE) target (i.e., 6.5 wt %), thus concluding that the total storage amount of hydrogen obtained at 303 K in graphite slitlike pores of carbon fibers is not sufficient yet.     

Solvation of sodium-chloride ion pair in water cluster at atmospheric conditions: grand canonical ensemble Monte Carlo simulation

Open statistical ensemble simulations are used to study the mechanism of nucleation of atmospheric water on sodium-chloride ion pair in a wide range of temperature and relative humidity values. The extended simple point-charge model is used for water molecules. Ions-water nonadditive interactions are taken into account by introducing the mutual polarization of ions and water in the field of each other. Gibbs free-energy variations are calculated from Na+-Cl- pair-correlation function and used as a criterion for determining the possible stable states of the cluster. In this relation, it was found that the dissociation of ion pairs in water clusters occurs even at vapor pressures of only a few millibars. In the conditions under consideration solvent-separated ion-pair states are found to be more probable than contact ion-pair configurations. The susceptibilities of water and ions are found to play an essential role in the stabilization of ions at large separations. The structure of ion-induced clusters is analyzed in terms of binary correlation functions. The non-pair interactions influence essentially the structure of ion solvation shells. The results of simulation show that the separation of the charges in water clusters containing simple ions can take place under atmospheric conditions.     

A grand canonical Monte Carlo study of capillary condensation in mesoporous media: effect of the pore morphology and topology

We study by means of Grand Canonical Monte Carlo simulations the condensation and evaporation of argon at 77 K in nanoporous silica media of different morphology or topology. For each porous material, our results are compared with data obtained for regular cylindrical pores. We show that both the filling and emptying mechanisms are significantly affected by the presence of a constriction. The simulation data for a constricted pore closed at one end reproduces the asymmetrical shape of the hysteresis loop that is observed for many real disordered porous materials. The adsorption process is a quasicontinuous mechanism that corresponds to the filling of the different parts of the porous material, cavity, and constriction. In contrast, the desorption branch for this pore closed at one end is brutal because the evaporation of Ar atoms confined in the largest cavity is triggered by the evaporation of the fluid confined in the constriction (which isolates the cavity from the gas reservoir). This evaporation process conforms to the classical picture of "pore blocking effect" proposed by Everett many years ago. We also simulate Ar adsorption in a disordered porous medium, which mimics a Vycor mesoporous silica glass. The adsorption isotherm for this disordered porous material having both topological and morphological defects presents the same features as that for the constricted pore (quasicontinuous adsorption and steep desorption process). However, the larger degree of disorder of the Vycor surface enhances these main characteristics. Finally, we show that the effect of the disorder, topological and/or morphological, leads to a significant lowering of the capillary condensation pressure compared to that for regular cylindrical nanopores. Also, our results suggest that confined fluids isolated from the bulk reservoir evaporate at a pressure driven by the smallest size of the pore.     

Molecular dynamics simulation in the grand canonical ensemble

An extended system Hamiltonian is proposed to perform molecular dynamics (MD) simulation in the grand canonical ensemble. The Hamiltonian is similar to the one proposed by Lynch and Pettitt (Lynch and Pettitt, J Chem Phys 1997, 107, 8594), which consists of the kinetic and potential energies for real and fractional particles as well as the kinetic and potential energy terms for material and heat reservoirs interacting with the system. We perform a nonlinear scaling of the potential energy parameters of the fractional particle, as well as its mass to vary the number of particles dynamically. On the basis of the equations of motion derived from this Hamiltonian, an algorithm has been proposed for MD simulation at constant chemical potential. The algorithm has been tested for the ideal gas, for the Lennard-Jones fluid over a wide range of temperatures and densities, and for water. The results for the low-density Lennard-Jones fluid are compared with the predictions from a truncated virial equation of state. In the case of the dense Lennard-Jones fluid and water our predicted results are compared with the results reported using other available methods for the calculation of the chemical potential. The method is also applied to the case of vapor-liquid coexistence point predictions.     

Thermodynamic characterization of fluids confined in heterogeneous pores by monte carlo simulations in the grand canonical and the isobaric-isothermal ensembles

Materials presenting nanoscale porosity are able to condense gases in their structure. This "capillary condensation" phenomenon has been studied for more than one century. Theoretical models help to understand experimental results but fail in explaining all experimental features. Most of the time, the difficulties in making quantitative or even qualitative predictions are due to the geometric complexity of the porous materials, such as large pore size distribution, chemical heterogeneities, or pore interconnections. Numerical calculations (lattice gas models or molecular simulations) are of considerable interest to calculate the adsorption properties of a fluid confined in a porous model with characteristic sizes up to several tens of nanometers. For instance, the grand canonical Monte Carlo method allows one to compute the average amount of fluid adsorbed in the porous model as a function of the temperature and the chemical potential of the fluid. However, the grand potential, necessary for a complete characterization of the system, is not a direct output of the algorithm. It is shown in this paper that the use of the isobaric-isothermal (NPT) ensemble allows one to circumvent this problem; that is, it is possible to get in one single Monte Carlo run the absolute grand potential for any given thermodynamic state of the fluid. A simplified thermodynamic integration scheme is then used to evaluate the grand potential over the whole isotherm branch passing through this initially given point. Since the usual NPT technique is a priori limited to homogeneous pores, it is proposed, for the first time, to generalize this procedure to a pore presenting a chemical heterogeneity along its axis. The new method gives the same results as the previous for homogeneous pores and allows new predictions for chemically heterogeneous pores. Comparison with the full integration scheme shows that the proposed direct calculation is faster since it avoids multiple Monte Carlo runs and more precise because it avoids the possible cumulative errors of the integration procedure.