Sofia Calero

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.

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.

Investigation of Entropy effects during Sorption of Mixtures of Alkanes in MFI zeolite

AbstractWe have carried out a comprehensive study of sorption of mixtures of alkanes, in the 1–7 C atom range, in MFI zeolite usingconfigurational-bias Monte Carlo (CBMC) simulations. The isotherm characteristics of various binary, ternary and quaternary mixtureshave been investigated. Our studies show that two types of entropy effects have a significant influence on mixture sorption:1. Size entropy effects arise due to differences in the saturation loading of the pure components. Size entropy effects favour the componentwith the smaller number of C atoms because the smaller molecule finds it easier to fill in the “gaps” within the zeolite matrix at highmolecular loadings.2. Configurational entropyeffects come into play for mixtures of alkanes that differ in the degree of branching. For a mixture of linearand mono-methyl alkanes with the same number of C atoms, configurational entropy effects favour the linear isomer because suchmolecules “pack” more efficiently within the MFI matrix. For a mixture of mono-methyl and di-methyl alkanes with the same numberof C atoms, configurational entropy effects favour the single branched isomer. Configurational entropy effect comes into play whenthe loading exceeds four molecules per unit cell, when all the intersection sites are occupied, and results in the following hierarchy ofsorption strengths: linear alkanes mono-methylalkanes di-methylalkanes.In all cases, the mixture isotherms can be predicted with good accuracy using the ideal adsorbed solution theory (IAST).CBMC simulations of sorption of an 8-component mixture containingn-pentane (n-C

Understanding Gas-Induced Structural Deformation of ZIF-8.

ZIF-8 is a zeolitic imidazolate framework with very good thermal and chemical stability that opens up many applications that are not feasible by other metal-organic frameowrks (MOFs) and zeolites. Several works report the adsorption properties of ZIF-8 for strategic gases. However, despite the vast experimental corpus of data reported, there seems yet to be a dearth in the understanding of the gas adsorption properties. In this work we provide insights at a molecular level on the mechanisms governing the ZIF-8 structural deformation during molecular adsorption. We demonstrate that the ZIF-8 structural deformation during the adsorption of different molecules at cryogenic temperature goes beyond the gas-induced rotation of the imidazolate linkers. We combine experimental and simulation studies to demonstrate that this deformation is governed by the polarizability and molecular size and shape of the gases, and that the stepped adsorption behavior is defined by the packing arrangement of the guest inside the host.

Functionalisation of MOF open metal sites with pendant amines for CO2 capture

The present work deals with the study of the effect of functionalisation of open metal sites in [Cu3(btc)2] (btc = 1,3,5-benzenetricarboxylate) [HKUST-1] with bifunctional amines for CO2 adsorption under dry and humid conditions.

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,

Shape selectivity through entropy

Based on a comparison between measured and simulated adsorption properties, we demonstrate that a decrease in the Gibbs free energy of formation and adsorption—due to higher adsorption entropy—satisfactorily explains the selective production and adsorption of the most compact, branched paraffins in n-hexadecane hydroconversion in molecular sieves with pore diameters of ∼ 0.75 nm. Adsorption entropy is important because the pores are saturated with reactant, and because the adsorbed phase is not at gas-phase chemical equilibrium. This explanation supplants the traditional kinetic explanation involving changes in the Gibbs free energy of formation of the relevant transition states. Instead, we attribute the effect of molecular sieve structure on the branched paraffin yield to a redirection of the hydroisomerization reactions away from the gas-phase chemical equilibrium distribution, commensurate with the Gibbs free energy of adsorption of the isomers inside the pores. These shape-selective changes to the reaction rates appear to be as ubiquitous as those originating from steric constraints imposed on intracrystalline diffusion and reaction rates. This would make adsorption-induced changes in the Gibbs free energy of formation of reactants, intermediates, and products a missing cornerstone in traditional shape selectivity theory.  2003 Elsevier Science (USA). All rights reserved.

On the Mechanism Behind the Instability of Isoreticular Metal-Organic Frameworks (IRMOFs) in Humid Environments

Increasing the resistance to humid environments is mandatory for the implementation of isoreticular metal-organic frameworks (IRMOFs) in industry. To date, the causes behind the sensitivity of [Zn(4)(μ(4)-O)(μ-bdc)(3)](8)(IRMOF-1; bdc=1,4-benzenedicarboxylate) to water remain still open. A multiscale scheme that combines Monte Carlo simulations, density functional theory and first-principles Born-Oppenheimer molecular dynamics on IRMOF-1 was employed to unravel the underlying atomistic mechanism responsible for lattice disruption. At very low water contents, H(2)O molecules are isolated in the lattice but provoke a dynamic opening of the terephthalic acid, and the lattice collapse occurs at about 6% water weight at room temperature. The ability of Zn to form fivefold coordination spheres and the increasing basicity of water when forming clusters are responsible for the displacement of the organic linker. The present results pave the way for synthetic challenges with new target linkers that might provide more robust IRMOF structures.

Evaluation of various water models for simulation of adsorption in hydrophobic zeolites

We have performed a molecular simulation study on water adsorption in hydrophobic zeolites. The framework structures are truly periodic and therefore the Ewald summation is the natural choice for computing the Coulombic interactions. However, a few water models have been parameterised using this method. The adsorption results are extremely sensitive to the water model used, the framework positions in the orthorhombic structure and the atomic charges of the zeolite framework. This work provides insight into the identification of the potential limitations of the available force fields and models, and into the point charges used for the zeolite atoms, when they are applied to a highly hydrophobic system. We discuss feasible routes to conciliate simulation and experimental results.

Understanding Zeolite Catalysis: Inverse Shape Selectivity Revised

Reference EPFL-ARTICLE-200562doi:10.1002/1521-3773(20020715)41:14 3.0.CO;2-T Record created on 2014-08-14, modified on 2017-12-10