R. Demuynck

Light Olefin Diffusion during the MTO Process on H-SAPO-34: a Complex Interplay of Molecular Factors

P. Cnudde, R. Demuynck, S. Vandenbrande, M. Waroquier, G. Sastre, V. Van Speybroeck
JACS (Journal of the American Chemical Society)
2020
A1

Abstract 

The methanol-to-olefins process over H-SAPO-34 is characterized by its high shape selectivity toward light olefins. The catalyst is a supramolecular system consisting of nanometer-sized inorganic cages, decorated by Brønsted acid sites, in which organic compounds, mostly methylated benzene species, are trapped. These hydrocarbon pool species are essential to catalyze the methanol conversion but may also clog the pores. As such, diffusion of ethene and propene plays an essential role in determining the ultimate product selectivity. Enhanced sampling molecular dynamics simulations based on either force fields or density functional theory are used to determine how molecular factors influence the diffusion of light olefins through the 8-ring windows of H-SAPO-34. Our simulations show that diffusion through the 8-ring in general is a hindered process, corresponding to a hopping event of the diffusing molecule between neighboring cages. The loading of different methanol, alkene, and aromatic species in the cages may substantially slow down or facilitate the diffusion process. The presence of Brønsted acid sites in the 8-ring enhances the diffusion process due to the formation of a favorable π-complex host–guest interaction. Aromatic hydrocarbon pool species severely hinder the diffusion and their spatial distribution in the zeolite crystal may have a significant effect on the product selectivity. Herein, we unveil how molecular factors influence the diffusion of light olefins in a complex environment with confined hydrocarbon pool species, high olefin loadings, and the presence of acid sites by means of enhanced molecular dynamics simulations under operating conditions.

Modeling Gas Adsorption in Flexible Metal–Organic Frameworks via Hybrid Monte Carlo / Molecular Dynamics Schemes

S.M.J. Rogge, R. Goeminne, R. Demuynck, J.J. Gutiérrez-Sevillano, S. Vandenbrande, L. Vanduyfhuys, M. Waroquier, T. Verstraelen, V. Van Speybroeck
Advanced Theory and Simulations
2 (4), 1800177
2019
A1

Abstract 

Herein, a hybrid Monte Carlo (MC)/molecular dynamics (MD) simulation protocol that properly accounts for the extraordinary structural flexibility of metal–organic frameworks (MOFs) is developed and validated. This is vital to accurately predict gas adsorption isotherms and guest‐induced flexibility of these materials. First, the performance of three recent models to predict adsorption isotherms and flexibility in MOFs is critically investigated. While these methods succeed in providing qualitative insight in the gas adsorption process in MOFs, their accuracy remains limited as the intrinsic flexibility of these materials is very hard to account for. To overcome this challenge, a hybrid MC/MD simulation protocol that is specifically designed to handle the flexibility of the adsorbent, including the shape flexibility, is introduced, thereby unifying the strengths of the previous models. It is demonstrated that the application of this new protocol to the adsorption of neon, argon, xenon, methane, and carbon dioxide in MIL‐53(Al), a prototypical flexible MOF, substantially decreases the inaccuracy of the obtained adsorption isotherms and predicted guest‐induced flexibility. As a result, this method is ideally suited to rationalize the adsorption performance of flexible nanoporous materials at the molecular level, paving the way for the conscious design of MOFs as industrial adsorbents.

Gold Open Access

Protocol for Identifying Accurate Collective Variables in Enhanced Molecular Dynamics Simulations for the Description of Structural Transformations in Flexible Metal–Organic Frameworks

R. Demuynck, J. Wieme, S.M.J. Rogge, K. Dedecker, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck
Journal of Chemical Theory and Computation
14 (11), pp 5511–5526
2018
A1

Abstract 

Various kinds of flexibility have been observed in metal–organic frameworks, which may originate from the topology of the material or the presence of flexible ligands. The construction of free energy profiles describing the full dynamical behavior along the phase transition path is challenging since it is not trivial to identify collective variables able to identify all metastable states along the reaction path. In this work, a systematic three-step protocol to uniquely identify the dominant order parameters for structural transformations in flexible metal–organic frameworks and subsequently construct accurate free energy profiles is presented. Methodologically, this protocol is rooted in the time-structure based independent component analysis (tICA), a well-established statistical modeling technique embedded in the Markov state model methodology and often employed to study protein folding, that allows for the identification of the slowest order parameters characterizing the structural transformation. To ensure an unbiased and systematic identification of these order parameters, the tICA decomposition is performed based on information from a prior replica exchange (RE) simulation, as this technique enhances the sampling along all degrees of freedom of the system simultaneously. From this simulation, the tICA procedure extracts the order parameters—often structural parameters—that characterize the slowest transformations in the material. Subsequently, these order parameters are adopted in traditional enhanced sampling methods such as umbrella sampling, thermodynamic integration, and variationally enhanced sampling to construct accurate free energy profiles capturing the flexibility in these nanoporous materials. In this work, the applicability of this tICA-RE protocol is demonstrated by determining the slowest order parameters in both MIL-53(Al) and CAU-13, which exhibit a strongly different type of flexibility. The obtained free energy profiles as a function of this extracted order parameter are furthermore compared to the profiles obtained when adopting less-suited collective variables, indicating the importance of systematically selecting the relevant order parameters to construct accurate free energy profiles for flexible metal–organic frameworks, which is in correspondence with experimental findings. The method succeeds in mapping the full free energy surface in terms of appropriate collective variables for MOFs exhibiting linker flexibility. For CAU-13, we show the decreased stability of the closed pore phase by systematically adding adsorbed xylene molecules in the framework.

On the intrinsic dynamic nature of the rigid UiO-66 metal-organic framework

J. Hajek, C. Caratelli, R. Demuynck, K. De Wispelaere, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck
Chemical Science
9 (10), 2723-2732
2018
A1

Abstract 

UiO-66 is a showcase example of an extremely stable metal–organic framework, which maintains its structural integrity during activation processes such as linker exchange and dehydration. The framework can even accommodate a substantial number of defects without compromising its stability. These observations point to an intrinsic dynamic flexibility of the framework, related to changes in the coordination number of the zirconium atoms. Herein we follow the dynamics of the framework in situ, by means of enhanced sampling molecular dynamics simulations such as umbrella sampling, during an activation process, where the coordination number of the bridging hydroxyl groups capped in the inorganic Zr6(μ3-O)4(μ3-OH)4 brick is reduced from three to one. Such a reduction in the coordination number occurs during the dehydration process and in other processes where defects are formed. We observe a remarkable fast response of the system upon structural changes of the hydroxyl group. Internal deformation modes are detected, which point to linker decoordination and recoordination. Detached linkers may be stabilized by hydrogen bonds with hydroxyl groups of the inorganic brick, which gives evidence for an intrinsic dynamic acidity even in the absence of protic guest molecules. Our observations yield a major step forward in the understanding on the molecular level of activation processes realized experimentally but that is hard to track on a purely experimental basis.

Open Access version available at UGent repository
Green Open Access

How chain length and branching influence the alkene cracking reactivity on H-ZSM-5

P. Cnudde, K. De Wispelaere, L. Vanduyfhuys, R. Demuynck, J. Van der Mynsbrugge, M. Waroquier, V. Van Speybroeck
ACS Catalysis
8, 9579 − 9595
2018
A1

Abstract 

Catalytic alkene cracking on H-ZSM-5 involves a complex reaction network with many possible reaction routes and often elusive intermediates. Herein, advanced molecular dynamics simulations at 773 K, a typical cracking temperature, are performed to clarify the nature of the intermediates and to elucidate dominant cracking pathways at operating conditions. A series of C4-C8 alkene intermediates are investigated to evaluate the influence of chain length and degree of branching on their stability. Our simulations reveal that linear, secondary carbenium ions are relatively unstable, although their lifetime increases with carbon number. Tertiary carbenium ions, on the other hand, are shown to be very stable, irrespective of the chain length. Highly branched carbenium ions, though, tend to rapidly rearrange into more stable cationic species, either via cracking or isomerization reactions. Dominant cracking pathways were determined by combining these insights on carbenium ion stability with intrinsic free energy barriers for various octene β-scission reactions, determined via umbrella sampling simulations at operating temperature (773 K). Cracking modes A (3° → 3°) and B2 (3° → 2°) are expected to be dominant at operating conditions, whereas modes B1 (2° → 3°), C (2° → 2°), D2 (2° → 1°) and E2 (3° → 1°) are expected to be less important. All β-scission modes in which a transition state with primary carbocation character is involved have high intrinsic free energy barriers. Reactions starting from secondary carbenium ions will contribute less as these intermediates are short living at the high cracking temperature. Our results show the importance of simulations at operating conditions to properly evaluate the carbenium ion stability for β-scission reactions and to assess the mobility of all species in the pores of the zeolite.

Open Access version available at UGent repository
Gold Open Access

The Importance of Cell Shape Sampling To Accurately Predict Flexibility in Metal-Organic Frameworks

S.M.J. Rogge, S. Caroes, R. Demuynck, M. Waroquier, V. Van Speybroeck, A. Ghysels
Journal of Chemical Theory and Computation
14 (3), 1186-1197
2018
A1

Abstract 

In this work, the influence of cell shape sampling on the predicted stability of the different metastable phases in flexible metal–organic frameworks at finite temperatures is investigated. The influence on the free energy by neglecting cell shape sampling is quantified for the prototypical MIL-53(Al) and the topical DUT-49(Cu). This goal is achieved by constructing free energy profiles in ensembles either in which the phase space associated with the cell shape is sampled explicitly or in which the cell shape is kept fixed. When neglecting cell shape sampling, thermodynamic integration of the hydrostatic pressure yields unreliable free energy profiles that depend on the choice of the fixed cell shape. In this work, we extend the thermodynamic integration procedure via the introduction of a generalized pressure, derived from the Lagrangian strain tensor and the second Piola–Kirchhoff tensor. Using this generalized procedure, the dependence on the unit cell shape can be eliminated, and the inaccuracy in free energy stemming from the lack of cell shape sampling can be uniquely quantified. Finally, it is shown that the inaccuracy in free energy when fixing the cell shape at room temperature stems mainly from entropic contributions for both MIL-53(Al) and DUT-49(Cu).

Efficient Construction of Free Energy Profiles of Breathing Metal-Organic Frameworks Using Advanced Molecular Dynamics Simulations

R. Demuynck, S.M.J. Rogge, L. Vanduyfhuys, J. Wieme, M. Waroquier, V. Van Speybroeck
Journal of Chemical Theory and Computation (JCTC)
13 (12), 5861-5873
2017
A1

Abstract 

In order to reliably predict and understand the breathing behavior of highly flexible metal–organic frameworks from thermodynamic considerations, an accurate estimation of the free energy difference between their different metastable states is a prerequisite. Herein, a variety of free energy estimation methods are thoroughly tested for their ability to construct the free energy profile as a function of the unit cell volume of MIL-53(Al). The methods comprise free energy perturbation, thermodynamic integration, umbrella sampling, metadynamics, and variationally enhanced sampling. A series of molecular dynamics simulations have been performed in the frame of each of the five methods to describe structural transformations in flexible materials with the volume as the collective variable, which offers a unique opportunity to assess their computational efficiency. Subsequently, the most efficient method, umbrella sampling, is used to construct an accurate free energy profile at different temperatures for MIL-53(Al) from first principles at the PBE+D3(BJ) level of theory. This study yields insight into the importance of the different aspects such as entropy contributions and anharmonic contributions on the resulting free energy profile. As such, this thorough study provides unparalleled insight in the thermodynamics of the large structural deformations of flexible materials.

Open Access version available at UGent repository
Gold Open Access

Semi-Analytical mean-field model for predicting breathing in Metal-Organic Frameworks

L. Vanduyfhuys, A. Ghysels, S.M.J. Rogge, R. Demuynck, V. Van Speybroeck
Molecular Simulation
41, 16-17, 1311-1328
2015
A1

Abstract 

A new semi-analytical model is proposed to rationalize breathing of MIL-53 type materials. The model is applied on two case studies, the guest-induced breathing of MIL-53(Cr) with CO 2 and CH 4 , and the phase transformations for MIL-53(Al) upon xenon adsorption. Experimentally, MIL-53(Cr) breathes upon CO 2 adsorption, which was not observed for CH 4 . This result could be ascribed to the stronger interaction of carbon dioxide with the host matrix. For MIL-53(Al) a phase transition from the large pore phase could be enforced to an intermediate phase with volumes of about 1160 − 1300 A, which corresponds well to the phase observed experimentally upon xenon adsorption. Our thermodynamic model correlates nicely with the adsorption pressure model proposed by Coudert et al. Furthermore the model can predict breathing behavior of other flexible materials, if the user can determine the free energy of the empty host, the interaction energy between a guest molecule and the host matrix and the pore volume accessible to the guest molecules. This will allow to generate the osmotic potential from which the equilibria can be deduced and the anticipated experimentally observed phase may be predicted.

Open Access version available at UGent repository

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