iRASPA: GPU-accelerated visualization software for materials scientists

A new macOS software package, iRASPA, for visualisation and editing of materials is presented. iRASPA is a document-based app that manages multiple documents with each document containing a unique set of data that is stored in a file located either in the application sandbox or in iCloud drive. The latter allows collaboration on a shared document (on High Sierra). A document contains a gallery of projects that show off the main features, a CloudKit-based access to the CoRE MOF database (approximately 8000 structures), and local projects of the user. Each project contains a scene of one or more structures that can initially be read from CIF, PDB or XYZ-files, or made from scratch. Main features of iRASPA are: structure creation and editing, pictures and movies, ambient occlusion and high-dynamic range rendering, collage of structures, (transparent) adsorption surfaces, cell replicas and supercells, symmetry operations like space group and primitive cell detection, screening of structures using user-defined predicates, and GPU-computation of helium void fraction and surface areas in a matter of seconds. Leveraging the latest graphics technologies like Metal, iRASPA can render hundreds of thousands of atoms (including ambient occlusion) with stunning performance. The software is freely available from the Mac App Store.Engineering Thermodynamic

Improving the accuracy of computing chemical potentials in CFCMC simulations

The CFCMC simulation methodology considers an expanded ensemble to solve the problem of low insertion/deletion acceptance probabilities in open ensembles. It allows for a direct calculation of the chemical potential by binning of the coupling parameter λ and using the probabilities p(λ = 0) and p(λ = 1), which require extrapolation. Here, we show that this extrapolation leads to systematic errors when the distribution p(λ) is steep. We propose an alternative binning scheme which improves the accuracy of computed chemical potentials. We also investigate the use of multiple fractional molecules needed in simulations of multiple components, and show that these fractional molecules are very weakly correlated and that calculations of chemical potentials are not affected. The statistics of Boltzmann averages in systems with multiple fractional molecules is shown to be poor. Good agreement is found between CFCMC averages (uncorrected for the bias) and Boltzmann averages when the number of fractional molecules is less than 1% of the total number of all molecules. We found that, in dense systems, biased averages have a smaller uncertainty compared to Boltzmann averages.Engineering Thermodynamic

Polarizable force field for CO₂ in M-MOF-74 derived from quantum mechanics

On the short term, carbon capture is a viable solution to reduce human-induced CO2 emissions, which requires an energy efficient separation of CO2. Metal-organic frameworks (MOFs) may offer opportunities for carbon capture and other industrially relevant separations. Especially, MOFs with embedded open metal sites have been shown to be promising. Molecular simulation is a useful tool to predict the performance of MOFs even before the synthesis of the material. This reduces the experimental effort, and the selection process of the most suitable MOF for a particular application can be accelerated. To describe the interactions between open metal sites and guest molecules in molecular simulation is challenging. Polarizable force fields have potential to improve the description of such specific interactions. Previously, we tested the applicability of polarizable force fields for CO2 in M-MOF-74 by verifying the ability to reproduce experimental measurements. Here, we develop a predictive polarizable force field for CO2 in M-MOF-74 (M = Co, Fe, Mg, Mn, Ni, Zn) without the requirement of experimental data. The force field is derived from energies predicted from quantum mechanics. The procedure is easily transferable to other MOFs. To incorporate explicit polarization, the induced dipole method is applied between the framework and the guest molecule. Atomic polarizabilities are assigned according to the literature. Only the Lennard-Jones parameters of the open metal sites are parameterized to reproduce energies from quantum mechanics. The created polarizable force field for CO2 in M-MOF-74 can describe the adsorption well and even better than that in our previous work.Engineering Thermodynamic

Multiple Free Energy Calculations from Single State Point Continuous Fractional Component Monte Carlo Simulation Using Umbrella Sampling

We introduce an alternative method to perform free energy calculations for mixtures at multiple temperatures and pressures from a single simulation, by combining umbrella sampling and the continuous fractional component Monte Carlo method. One can perform a simulation of a mixture at a certain pressure and temperature and accurately compute the chemical potential at other pressures and temperatures close to the simulation conditions. This method has the following advantages: (1) Accurate estimates of the chemical potential as a function of pressure and temperature are obtained from a single state simulation without additional postprocessing. This can potentially reduce the number of simulations of a system for free energy calculations for a specific temperature and/or pressure range. (2) Partial molar volumes and enthalpies are obtained directly from the estimated chemical potentials. We tested our method for a Lennard-Jones system, aqueous mixtures of methanol at T = 298 K and P = 1 bar, and a mixture of ammonia, nitrogen, and hydrogen at T = 573 K and P = 800 bar. For pure methanol (N = 410 molecules), we observed that the estimated chemical potentials from umbrella sampling are in excellent agreement with the reference values obtained from independent simulations, for ΔT = ±15 K and ΔP = 100 bar (with respect to the simulated system). For larger systems, this range becomes smaller because the relative fluctuations of energy and volume become smaller. Without sufficient overlap, the performance of the method will become poor especially for nonlinear variations of the chemical potential.Engineering Thermodynamic

Chemical potentials of water, methanol, carbon dioxide and hydrogen sulphide at low temperatures using continuous fractional component Gibbs ensemble Monte Carlo

Chemical potentials of coexisting gas and liquid phases for water, methanol, hydrogen sulphide and carbon dioxide for the temperature range (Formula presented.) K to (Formula presented.) K are computed using two different methodologies: (1) Widom’s test particle insertion (WTPI) method in the conventional Gibbs Ensemble (GE), and (2) the Continuous Fractional Component Gibbs Ensemble Monte Carlo (CFCGE MC) method. It is shown that the WTPI method fails to accurately compute the chemical potentials of water and methanol in the liquid phase at low temperatures, while accurate chemical potentials in the liquid phase are computed using CFCGE MC method. For the CFCGE MC method, the statistical uncertainty for computed chemical potentials of water and methanol in the liquid phase are considerably smaller compared to the WTPI method. For the water models considered in this study (SPC, TIP3P-EW, TIP4P-EW, TIP5P-EW), computed excess chemical potentials based on three-site models are in better agreement with the chemical potentials computed from an empirical equation of state from the NIST database. For water, orientational biasing is applied during test particle insertion to check whether certain orientations of test particle are energetically unfavourable. A two-dimensional Overlapping Distribution Method (ODM) in the NVT ensemble is derived for this purpose. It is shown that failure of the WTPI method for systems with a strong hydrogen bonding network does not depend on orientation of the test molecule in that system. For all systems in this study, the WTPI method breaks down when the void fraction of the system drops below approximately 0.50.Engineering Thermodynamic

Effects of Framework Flexibility on the Adsorption and Diffusion of Aromatics in MFI-Type Zeolites

We systematically study how the degree of framework flexibility affects the adsorption and diffusion of aromatics in MFI-type zeolites as computed by Monte Carlo simulations. It is observed that as the framework is more flexible, the zeolite structure is inherently changed. We have found that framework flexibility has a significant effect on the adsorption of aromatics in MFI-type zeolites, especially at high pressure. Framework flexibility allows the zeolite framework to accommodate to the presence of guest aromatic molecules. For very flexible zeolite frameworks, loadings up to two times larger than that in a rigid zeolite framework are obtained at a given pressure. We assessed the "flexible snapshot"method, which captures framework flexibility using independent snapshots of the framework. We have found that this method only works well when the loadings are low. This suggests that the effect of the guest molecules on the zeolite framework is important. Framework flexibility lowers the free-energy barriers between low energy states, increasing the rate of diffusion of aromatics in the straight channel of MFI-type zeolites for many orders of magnitude compared to a rigid zeolite framework. The simulations show that framework flexibility should not be neglected and that it significantly affects the diffusion and adsorption properties of aromatics in an MFI-type zeolite. Engineering Thermodynamic

Competitive Adsorption of Xylenes at Chemical Equilibrium in Zeolites

The separation of xylenes is one of the most important processes in the petrochemical industry. In this article, the competitive adsorption from a fluid-phase mixture of xylenes in zeolites is studied. Adsorption from both vapor and liquid phases is considered. Computations of adsorption of pure xylenes and a mixture of xylenes at chemical equilibrium in several zeolite types at 250 °C are performed by Monte Carlo simulations. It is observed that shape and size selectivity entropic effects are predominant for small one-dimensional systems. Entropic effects due to the efficient arrangement of xylenes become relevant for large one-dimensional systems. For zeolites with two intersecting channels, the selectivity is determined by a competition between enthalpic and entropic effects. Such effects are related to the orientation of the methyl groups of the xylenes. m-Xylene is preferentially adsorbed if xylenes fit tightly in the intersection of the channels. If the intersection is much larger than the adsorbed molecules, p-xylene is preferentially adsorbed. This study provides insight into how the zeolite topology can influence the competitive adsorption and selectivity of xylenes at reaction conditions. Different selectivities are observed when a vapor phase is adsorbed compared to the adsorption from a liquid phase. These insight have a direct impact on the design criteria for future applications of zeolites in the industry. MRE-type and AFI-type zeolites exclusively adsorb p-xylene and o-xylene from the mixture of xylenes in the liquid phase, respectively. These zeolite types show potential to be used as high-performing molecular sieves for xylene separation and catalysis.Engineering Thermodynamic

Computation of thermodynamic properties in the continuous fractional component Monte Carlo Gibbs ensemble

It is shown that ensemble averages computed in the Gibbs Ensemble with Continuous Fractional Component Monte Carlo (CFCMC GE) are different from those computed in the conventional Gibbs Ensemble (GE). However, it is possible to compute averages corresponding to the conventional GE while performing simulations in the CFCMC GE. In this way, one can benefit from the nice features of CFCMC GE (e.g. more efficient particle exchange) and at the same time compute the ensemble averages that correspond to the conventional GE. As a case study, the equilibrium pressure and densities of the systems of 256 and 512 LJ particles at different reduced temperatures ((Formula presented.)) are computed in the conventional GE and CFCMC GE. The validity of the expressions derived for computation of the thermodynamic pressure and densities corresponding to the conventional GE and computed in the CFCMC GE is examined numerically. The thermodynamic pressure in the conventional GE and CFCMC GE typically differs by at most 4%. It is shown that a very good estimate of the average pressure and densities corresponding to the conventional GE can be obtained by performing simulation in CFCMC GE and ignoring the contributions of the fractional molecule. It is also shown that the fractional molecule does not have an influence on the structure of the liquid, even for very small system sizes (e.g. 40 particles). The approach used here to compute the equilibrium pressure and densities of the conventional GE using the CFCMC GE can be easily extended to other thermodynamic properties and other ensembles.Accepted Author ManuscriptEngineering Thermodynamic

Recent advances in the continuous fractional component Monte Carlo methodology

In this paper, we review recent advances in the Continuous Fractional Component Monte Carlo (CFCMC) methodology and present a historic overview of the most important developments that have led to this method. The CFCMC method has gained attention for Monte Carlo simulations of adsorption at high loading, and phase and reaction equilibria of dense systems. It has recently been extended to reactive systems. The main features of the CFCMC method are: (1) Increased molecule exchange efficiency between different phases in single and multicomponent (reactive) systems, which improves the efficiency and accuracy of phase equilibria simulations at high densities; (2) Direct calculation of the chemical potential from a single simulation; (3) Direct calculation of partial molar properties from a single simulation. The developed simulation techniques are incorporated in the open-source molecular simulation software Brick-CFCMC.Engineering Thermodynamic

Adsorption equilibrium of nitrogen dioxide in porous materials

The effect of confinement on the equilibrium reactive system containing nitrogen dioxide and dinitrogen tetroxide is studied by molecular simulation and the reactive Monte Carlo (RxMC) approach. The bulk-phase reaction was successfully reproduced and five all-silica zeolites (i.e. FAU, FER, MFI, MOR, and TON) with different topologies were selected to study their adoption behavior. Dinitrogen tetroxide showed a stronger affinity than nitrogen dioxide in all the zeolites due to size effects, but exclusive adsorption sites in MOR allowed the adsorption of nitrogen dioxide with no competition at these sites. From the study of the adsorption isotherms and isobars of the reacting mixture, confinement enhanced the formation of dimers over the full range of pressure and temperature, finding the largest deviations from bulk fractions at low temperature and high pressure. The channel size and shape of the zeolite have a noticeable influence on the dinitrogen tetroxide formation, being more important in MFI, closely followed by TON and MOR, and finally FER and FAU. Preferential adsorption sites in MOR lead to an unusually strong selective adsorption towards nitrogen dioxide, demonstrating that the topological structure has a crucial influence on the composition of the mixture and must be carefully considered in systems containing nitrogen dioxide.Accepted Author ManuscriptEngineering Thermodynamic