L. Vanduyfhuys

Thermodynamic modeling of the selective adsorption of carbon dioxide over methane in the mechanically constrained breathing MIL-53(Cr)

L. Vanduyfhuys, G. Maurin
Advanced Theory and Simulations
1900124
2019
A1

Abstract 

The coadsorption of CO2/CH4 in the breathing MIL-53(Cr) under the application of an additional mechanical pressure is investigated through the use of an extended thermodynamic mean-field model. The focus is on the breathing behavior, negative gas adsorption (NGA), and selective adsorption of CO2 as well as to what degree the application of mechanical pressure influences this behavior. To this end, phase diagrams, coadsorption isotherms are constructed and the CO 2 /CH 4 selectivity is computed in terms of the vapor pressure of methane and carbon dioxide as well as the mechanical pressure. As a result, it was found that NGA can be induced by coadsorption of CO2 /CH4 gas mixtures with certain molar compositions. Finally, a specific adsorption/desorption cycle, which includes the application of an additional mechanical pressure, is proposed to allow for an increased CO2/CH4 selectivity as well as for an expected less energy demanding CO2 desorption step.

DOI 

http://dx.doi.org/10.1002/adts.201900124

Thermal Engineering of Metal-Organic Frameworks for Adsorption Applications: A Molecular Simulations Perspective

J. Wieme, S. Vandenbrande, A. Lamaire, V. Kapil, L. Vanduyfhuys, V. Van Speybroeck
ACS Applied Materials & Interfaces
11 (42), 38697-38707
2019
A1

Abstract 

Thermal engineering of metal-organic frameworks (MOFs) for adsorption-based applications is very topical in view of their industrial potential, especially since heat management and thermal stability have been identified as important obstacles. Hence, a fundamental understanding of the structural and chemical features underpinning their intrinsic thermal properties is highly sought-after. Herein, we investigate the nanoscale behavior of a diverse set of frameworks using molecular simulation techniques and critically compare properties such as thermal conductivity, heat capacity and thermal expansion with other material classes. Furthermore, we propose a hypothetical thermodynamic cycle to estimate the temperature rise associated with adsorption for the most important greenhouse and energy-related gases (CO2 and CH4). This macroscopic response on the heat of adsorption connects the intrinsic thermal properties with the adsorption properties, and allows us to evaluate their importance.

DOI 

http://dx.doi.org/10.1021/acsami.9b12533

Pillared-layered metal-organic frameworks for mechanical energy storage applications

J. Wieme, S.M.J. Rogge, P.G. Yot, L. Vanduyfhuys, S.-K. Lee, J.-S. Chang, M. Waroquier, G. Maurin, V. Van Speybroeck
Journal of Materials Chemistry A
7 (39), 22663-22674
2019
A1

Abstract 

Herein we explore the unique potential of pillared-layered metal–organic frameworks of the DMOF-1 family for mechanical energy storage applications. In this work, we theoretically predict for the guest-free DMOF-1 a new contracted phase by exerting an external mechanical pressure of more than 200 MPa with respect to the stable phase at atmospheric pressure. The breathing transition is accompanied by a very large volume contraction of about 40%. The high transition pressures and associated volume changes make these materials highly promising with an outstanding mechanical energy work. Furthermore, we show that changing the nature of the metal allows to tune the behavior under mechanical pressure. The various phases were revealed by a combination of periodic density-functional theory calculations, force field molecular dynamics simulations and mercury intrusion experiments for DMOF-1(Zn) and DMOF-1(Cu). The combined experimental and theoretical approach allowed to discover the potential of these materials for new technological developments.

Gold Open Access

DOI 

http://dx.doi.org/10.1039/C9TA01586H

Insight into the role of water on the methylation of hexamethylbenzene in H-SAPO-34 from first principle molecular dynamics simulations

S. Bailleul, S.M.J. Rogge, L. Vanduyfhuys, V. Van Speybroeck
ChemCatChem
11 (16), 3993-4010
2019
A1

Abstract 

The methylation of hexamethylbenzene with methanol is one of the key reactions in the methanol‐to‐olefins hydrocarbon pool reaction cycle taking place over the industrially relevant H‐SAPO‐34 zeolite. This methylation reaction can occur either via a concerted or via a stepwise mechanism, the latter being the preferred pathway at higher temperatures. Herein, we systematically investigate how a complex reaction environment with additional water molecules and higher concentrations of Brønsted acid sites in the zeolite impacts the reaction mechanism. To this end, first principle molecular dynamics simulations are performed using enhanced sampling methods to characterize the reactants and products in the catalyst pores and to construct the free energy profiles. The most prominent effect of the dynamic sampling of the reaction path is the stabilization of the product region where water is formed, which can either move freely in the pores of the zeolite or be stabilized through hydrogen bonding with the other protic molecules. These protic molecules also stabilize the deprotonated Brønsted acid site, created due to the formation of the heptamethylbenzenium cation, via a Grotthuss‐type mechanism. Our results provide fundamental insight in the experimental parameters that impact the methylation of hexamethylbenzene in H‐SAPO‐34, especially highlighting and rationalizing the crucial role of water in one of the main reactions of the aromatics‐based reaction cycle.

Gold Open Access

DOI 

http://dx.doi.org/10.1002/cctc.201900618

The impact of lattice vibrations on the macroscopic breathing behavior of MIL-53(Al)

A.E.J. Hoffman, J. Wieme, S.M.J. Rogge, L. Vanduyfhuys, V. Van Speybroeck
Zeitschrift für Kristallographie - Crystalline Materials
234 (7-8), 529-545
2019
A1

Abstract 

The mechanism inducing the breathing in flexible metal-organic frameworks, such as MIL-53(Al), is still not fully understood. Herein, the influence of lattice vibrations on the breathing transition in MIL-53(Al) is investigated to gain insight in this phenomenon. Through solid-state density-functional theory calculations, the volume-dependent IR spectrum is computed together with the volume-frequency relations of all vibrational modes. Furthermore, important thermodynamic properties such as the Helmholtz free energy, the specific heat capacity, the bulk modulus, and the volumetric thermal expansion coefficient are derived via these volume-frequency relations using the quasi-harmonic approximation. The simulations expose a general volume-dependency of the vibrations with wavenumbers above 300 cm−1 due to their localized nature. In contrast, a diverse set of volume-frequency relations are observed for vibrations in the terahertz region (< 300 cm−1) containing the vibrations exhibiting collective behavior. Some terahertz vibrations display large frequency differences over the computed volume range, induced by either repulsion or strain effects, potentially triggering the phase transformation. Finally, the impact of the lattice vibrations on the thermodynamic properties is investigated. This reveals that the closed pore to large pore phase transformation in MIL-53(Al) is mainly facilitated by terahertz vibrations inducing rotations of the organic linker, while the large pore to closed pore phase transformation relies on two framework-specific soft modes.

Gold Open Access

DOI 

http://dx.doi.org/10.1515/zkri-2018-2154

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

DOI 

http://dx.doi.org/10.1002/adts.201800177

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.

DOI 

http://dx.doi.org/10.1021/acs.jctc.8b00725

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

DOI 

http://dx.doi.org/10.1039/C7SC04947A

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

DOI 

http://dx.doi.org/10.1021/acscatal.8b01779

Extension of the QuickFF force field protocol for an improved accuracy of structural, vibrational, mechanical and thermal properties of Metal Organic Frameworks

L. Vanduyfhuys, S. Vandenbrande, J. Wieme, M. Waroquier, T. Verstraelen, V. Van Speybroeck
Journal of Computational Chemistry
39 (16), p. 999-1011
2018
A1

Abstract 

QuickFF was originally launched in 2015 to derive accurate force fields for isolated and complex molecular systems in a quick and easy way. Apart from the general applicability, the functionality was especially tested for metal-organic frameworks (MOFs), a class of hybrid materials consisting of organic and inorganic building blocks. Herein, we launch a new release of the QuickFF protocol which includes new major features to predict structural, vibrational, mechanical and thermal properties with greater accuracy, without compromising its robustness and transparant workflow. First, the ab initio data necessary for the fitting procedure may now also be derived from periodic models for the molecular system, as opposed to the earlier cluster-based models. This is essential for an accurate description of MOFs with one dimensional metal-oxide chains. Second, cross terms that couple internal coordinates (ICs) and anharmonic contributions for bond and bend terms are implemented. These features are essential for a proper description of vibrational and thermal properties. Third, the fitting scheme was modified to improve robustness and accuracy. The new features are tested on MIL-53(Al), MOF-5, CAU-13 and NOTT-300. As expected, periodic input data is proven to be essential for a correct description of structural, vibrational and thermodynamic properties of MIL-53(Al). Bulk moduli and thermal expansion coefficients of MOF-5 are very accurately reproduced by static and dynamic simulations using the newly derived force fields which include cross terms and anharmonic corrections. For the flexible materials CAU-13 and NOTT-300, the transition pressure is accurately
predicted provided cross terms are taken into account.

Open Access version available at UGent repository
Gold Open Access

DOI 

http://dx.doi.org/10.1002/jcc.25173

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