David Dubbeldam

RASPA: molecular simulation software for adsorption and diffusion in flexible nanoporous materials

A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Bakers minimisation. We show example applications of RASPA in computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, reaction systems and visualisation. The software is released under the GNU General Public License.

Heats of adsorption for seven gases in three metal - Organic frameworks: Systematic comparison of experiment and simulation

The heat of adsorption is an important parameter for gas separation and storage applications in porous materials such as metal-organic frameworks (MOFs). There are, however, few systematic studies available in the MOF literature. Many papers report results for only one MOF and often only for a single gas. In this work, systematic experimental measurements by TAP-2 are reported for the heats of adsorption of seven gases in three MOFs. The gases are Kr, Xe, N2, CO2, CH4, n-C4H10, and i-C4H10. The MOFs studied are IRMOF-1, IRMOF-3, and HKUST-1. The data set provides a valuable test for molecular simulation. The simulation results suggest that structural differences in HKUST-1 experimental samples may lead to differing heats of adsorption.

On the inner workings of Monte Carlo codes

We review state-of-the-art Monte Carlo (MC) techniques for computing fluid coexistence properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as zeolites and metal–organic frameworks. Conventional MC is discussed and compared to advanced techniques such as reactive MC, configurational-bias Monte Carlo and continuous fractional MC. The latter technique overcomes the problem of low insertion probabilities in open systems. Other modern methods are (hyper-)parallel tempering, Wang–Landau sampling and nested sampling. Details on the techniques and acceptance rules as well as to what systems these techniques can be applied are provided. We highlight consistency tests to help validate and debug MC codes.

The distributed ASCI Supercomputer project

The Distributed ASCI Supercomputer (DAS) is a homogeneous wide-area distributed system consisting of four cluster computers at different locations. DAS has been used for research on communication software, parallel languages and programming systems, schedulers, parallel applications, and distributed applications. The paper gives a preview of the most interesting research results obtained so far in the DAS project.

Computing the Heat of Adsorption using Molecular Simulations: The Effect of Strong Coulombic Interactions

Molecular simulations are an important tool for the study of adsorption of hydrocarbons in nanoporous materials such as zeolites. The heat of adsorption is an important thermodynamic quantity that can be measured both in experiments and molecular simulations, and therefore it is often used to investigate the quality of a force field for a certain guest-host (g - h) system. In molecular simulations, the heat of adsorption in zeolites is often computed using either of the following methods: (1) using the Clausius-Clapeyron equation, which requires the partial derivative of the pressure with respect to temperature at constant loading, (2) using the energy difference between the host with and without a single guest molecule present, and (3) from energy/particle fluctuations in the grand-canonical ensemble. To calculate the heat of adsorption from experiments (besides direct calorimetry), only the first method is usually applicable. Although the computation of the heat of adsorption is straightforward for all-silica zeolites, severe difficulties arise when applying the conventional methods to systems with nonframework cations present. The reason for this is that these nonframework cations have very strong Coulombic interactions with the zeolite. We will present an alternative method based on biased interactions of guest molecules that suffers less from these difficulties. This method requires only a single simulation of the host structure. In addition, we will review some of the other important issues concerning the handling of these strong Coulombic interactions in simulating the adsorption of guest molecules. It turns out that the recently proposed Wolf method ( J. Chem. Phys. 1999, 110 , 8254 ) performs poorly for zeolites as a large cutoff radius is needed for convergence.

Recent developments in the molecular modeling of diffusion in nanoporous materials

Molecular modeling has become a useful and widely used tool to predict diffusion coefficients of molecules adsorbed in the pores of zeolites and other nanoporous materials. These simulations also provide detailed, molecular-level information about sorbate structure, dynamics, and diffusion mechanisms. We review recent advances in this field, including prediction of various transport coefficients (Fickian, Onsager, Maxwell–Stefan) for single-component and multicomponent systems from equilibrium and non-equilibrium molecular dynamics (MD) simulations, elucidation of anomalous diffusion effects induced by the confining pore structure, and prediction of slow diffusion processes beyond the reach of MD simulations.

Separation and Molecular-Level Segregation of Complex Alkane Mixtures in Metal−Organic Frameworks

In this computational work we explore metal-organic frameworks (MOFs) for separating alkanes according to the degree of branching. We show that the structure MOF-1 shows an adsorption hierarchy for a 13-component light naphtha mixture precisely as desired for increasing the research octane number of gasoline. In addition we report an unusual molecular-level segregation of molecules based on their degree of branching.

Molecular simulation of loading dependent diffusion in nanoporous materials using extended dynamically corrected transition state theory

A dynamically corrected transition state theory method is presented that is capable of computing quantitatively the self-diffusivity of adsorbed molecules in confined systems at nonzero loading. This extension to traditional transition state theory is free of additional assumptions and yields a diffusivity identical to that obtained by conventional molecular-dynamics simulations. While molecular-dynamics calculations are limited to relatively fast diffusing molecules, our approach extends the range of accessible time scales significantly beyond currently available methods. We show results for methane, ethane, and propane in LTL- and LTA-type zeolites over a wide range of temperatures and loadings, and demonstrate the extensibility of the method to mixtures.

Molecular-level Insight into Unusual Low Pressure CO2 Affinity in Pillared Metal-Organic Frameworks

Fundamental insight into how low pressure adsorption properties are affected by chemical functionalization is critical to the development of next-generation porous materials for postcombustion CO2 capture. In this work, we present a systematic approach to understanding low pressure CO2 affinity in isostructural metal-organic frameworks (MOFs) using molecular simulations and apply it to obtain quantitative, molecular-level insight into interesting experimental low pressure adsorption trends in a series of pillared MOFs. Our experimental results show that increasing the number of nonpolar functional groups on the benzene dicarboxylate (BDC) linker in the pillared DMOF-1 [Zn2(BDC)2(DABCO)] structure is an effective way to tune the CO2 Henrys coefficient in this isostructural series. These findings are contrary to the common scenario where polar functional groups induce the greatest increase in low pressure affinity through polarization of the CO2 molecule. Instead, MOFs in this isostructural series containing nitro, hydroxyl, fluorine, chlorine, and bromine functional groups result in little increase to the low pressure CO2 affinity. Strong agreement between simulated and experimental Henrys coefficient values is obtained from simulations on representative structures, and a powerful yet simple approach involving the analysis of the simulated heats of adsorption, adsorbate density distributions, and minimum energy 0 K binding sites is presented to elucidate the intermolecular interactions governing these interesting trends. Through a combined experimental and simulation approach, we demonstrate how subtle, structure-specific differences in CO2 affinity induced by functionalization can be understood at the molecular-level through classical simulations. This work also illustrates how structure-property relationships resulting from chemical functionalization can be very specific to the topology and electrostatic environment in the structure of interest. Given the excellent agreement between experiments and simulation, predicted CO2 selectivities over N2, CH4, and CO are also investigated to demonstrate that methyl groups also provide the greatest increase in CO2 selectivity relative to the other functional groups. These results indicate that methyl ligand functionalization may be a promising approach for creating both water stable and CO2 selective variations of other MOFs for various industrial applications.

Computer‐Assisted Screening of Ordered Crystalline Nanoporous Adsorbents for Separation of Alkane Isomers

The separation of linear, mono-branched, and di-branchedisomers of alkanes is of significant importance in thepetrochemicalindustry. For example, thedi-branchedalkanesin the 5–7 carbon number range are preferred components ofhigh-octane gasoline. Their selective removal from the otherisomers produced in an alkane isomerization reactor can beachievedusingorderedcrystallinenanoporousmaterials,suchas zeolites, metal–organic frameworks (MOFs), covalentorganic frameworks (COFs), and zeolitic imidazolate frame-works (ZIFs), by exploiting subtle differences in molecularconfigurations. Literally, several thousands of such materialshave been synthesized, making the choice of adsorbenta daunting task. Our approach is to carry out molecularsimulations on a pre-screened list of more than 100 nano-porous structures. Our screening methodology demonstratesthat ZIF-77, whose synthesis was reported in 2008,