Center for Molecular Modeling - ERC DYNPOR H20ERC2015000301

Operando modeling of zeolite catalyzed reactions using first principle molecular dynamics simulations

mieke — Tue, 08 Aug 2023 11:40:10 +0000

V. Van Speybroeck, M. Bocus, P. Cnudde, L. Vanduyfhuys

ACS Catalysis

13, 17, 11455-11493

2023

Abstract

Within this Perspective, we critically reflect on the role of first-principles molecular dynamics (MD) simulations in unraveling the catalytic function within zeolites under operating conditions. First-principles MD simulations refer to methods where the dynamics of the nuclei is followed in time by integrating the Newtonian equations of motion on a potential energy surface that is determined by solving the quantum-mechanical many-body problem for the electrons. Catalytic solids used in industrial applications show an intriguing high degree of complexity, with phenomena taking place at a broad range of length and time scales. Additionally, the state and function of a catalyst critically depend on the operating conditions, such as temperature, moisture, presence of water, etc. Herein we show by means of a series of exemplary cases how first-principles MD simulations are instrumental to unravel the catalyst complexity at the molecular scale. Examples show how the nature of reactive species at higher catalytic temperatures may drastically change compared to species at lower temperatures and how the nature of active sites may dynamically change upon exposure to water. To simulate rare events, first-principles MD simulations need to be used in combination with enhanced sampling techniques to efficiently sample low-probability regions of phase space. Using these techniques, it is shown how competitive pathways at operating conditions can be discovered and how broad transition state regions can be explored. Interestingly, such simulations can also be used to study hindered diffusion under operating conditions. The cases shown clearly illustrate how first-principles MD simulations reveal insights into the catalytic function at operating conditions, which could not be discovered using static or local approaches where only a few points are considered on the potential energy surface (PES). Despite these advantages, some major hurdles still exist to fully integrate first-principles MD methods in a standard computational catalytic workflow or to use the output of MD simulations as input for multiple length/time scale methods that aim to bridge to the reactor scale. First of all, methods are needed that allow us to evaluate the interatomic forces with quantum-mechanical accuracy, albeit at a much lower computational cost compared to currently used density functional theory (DFT) methods. The use of DFT limits the currently attainable length/time scales to hundreds of picoseconds and a few nanometers, which are much smaller than realistic catalyst particle dimensions and time scales encountered in the catalysis process. One solution could be to construct machine learning potentials (MLPs), where a numerical potential is derived from underlying quantum-mechanical data, which could be used in subsequent MD simulations. As such, much longer length and time scales could be reached; however, quite some research is still necessary to construct MLPs for the complex systems encountered in industrially used catalysts. Second, most currently used enhanced sampling techniques in catalysis make use of collective variables (CVs), which are mostly determined based on chemical intuition. To explore complex reactive networks with MD simulations, methods are needed that allow the automatic discovery of CVs or methods that do not rely on a priori definition of CVs. Recently, various data-driven methods have been proposed, which could be explored for complex catalytic systems. Lastly, first-principles MD methods are currently mostly used to investigate local reactive events. We hope that with the rise of data-driven methods and more efficient methods to describe the PES, first-principles MD methods will in the future also be able to describe longer length/time scale processes in catalysis. This might lead to a consistent dynamic description of all steps─diffusion, adsorption, and reaction─as they take place at the catalyst particle level.

DOI

http://dx.doi.org/10.1021/acscatal.3c01945

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van-speybroeck-et-al-2023-operando-modeling-of-zeolite-catalyzed-reactions-using-first-principles-molecular-dynamics.pdf

Challenges in modelling dynamic processes in realistic nanostructured materials at operating conditions

leen — Mon, 22 May 2023 07:08:46 +0000

V. Van Speybroeck

Philosophical Transactions of the Royal Society A

381, 2250 & 20220239

2023

Abstract

The question is addressed in how far current modelling strategies are capable of modelling dynamic phenomena in realistic nanostructured materials at operating conditions. Nanostructured materials used in applications are far from perfect; they possess a broad range of heterogeneities in space and time extending over several orders of magnitude. Spatial heterogeneities from the subnanometre to the micrometre scale in crystal particles with a finite size and specific morphology, impact the material's dynamics. Furthermore, the material's functional behaviour is largely determined by the operating conditions. Currently, there exists a huge length–time scale gap between attainable theoretical length–time scales and experimentally relevant scales. Within this perspective, three key challenges are highlighted within the molecular modelling chain to bridge this length–time scale gap. Methods are needed that enable (i) building structural models for realistic crystal particles having mesoscale dimensions with isolated defects, correlated nanoregions, mesoporosity, internal and external surfaces; (ii) the evaluation of interatomic forces with quantum mechanical accuracy albeit at much lower computational cost than the currently used density functional theory methods and (iii) derivation of the kinetics of phenomena taking place in a multi-length–time scale window to obtain an overall view of the dynamics of the process.

This article is part of a discussion meeting issue ‘Supercomputing simulations of advanced materials’.

DOI

https://doi.org/10.1098/rsta.2022.0239

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An embedded interfacial network stabilizes inorganic CsPbI3 perovskite thin films

tbraeckevelt — Wed, 07 Dec 2022 10:38:53 +0000

J.A. Steele, T. Braeckevelt, V. Prakasam, G. Degutis, H. Yuan, H. Jin, E. Solano, P. Puech, S. Basak, M.I. Pintor-Monroy, H. Van Gorp, G. Fleury, R.X. Yang, Z. Lin, H. Huang, E. Debroye, D. Chernyshov, B. Chen, M. Wei, Y. Hou, R. Gehlhaar, J. Genoe, S. De Feyter, S.M.J. Rogge, A. Walsh, E.H. Sargent, P. Yang, J. Hofkens, V. Van Speybroeck, M.B.J. Roeffaers

Nature Communications

13, 7513

2022

Abstract

The black perovskite phase of CsPbI₃ is promising for optoelectronic applications; however, it is unstable under ambient conditions, transforming within minutes into an optically inactive yellow phase, a fact that has so far prevented its widespread adoption. Here we use coarse photolithography to embed a PbI₂-based interfacial microstructure into otherwise-unstable CsPbI₃ perovskite thin films and devices. Films fitted with a tessellating microgrid are rendered resistant to moisture-triggered decay and exhibit enhanced long-term stability of the black phase (beyond 2.5 years in a dry environment), due to increasing the phase transition energy barrier and limiting the spread of potential yellow phase formation to structurally isolated domains of the grid. This stabilizing effect is readily achieved at the device level, where unencapsulated CsPbI₃ perovskite photodetectors display ambient-stable operation. These findings provide insights into the nature of phase destabilization in emerging CsPbI₃ perovskite devices and demonstrate an effective stabilization procedure which is entirely orthogonal to existing approaches.

DOI

https://doi.org/10.1038/s41467-022-35255-9

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How water and ion mobility affect the NMR fingerprints of the hydrated JBW zeolite: a combined computational-experimental investigation

alexander — Wed, 24 Aug 2022 07:27:54 +0000

S. Vanlommel, A.E.J. Hoffman, S. Smet, S. Radhakrishnan, K. Asselman, C. V. Chandran, E. Breynaert, C. Kirschhock, J.A. Martens, V. Van Speybroeck

Chemistry - A European Journal

28, 68, e202202621

2022

Abstract

An important aspect within zeolite synthesis is to make fully tunable framework materials with controlled aluminium distribution. A major challenge in characterising these zeolites at operating conditions is the presence of water. In this work, we investigate the effect of hydration on the 27 Al NMR parameters of the ultracrystalline K,Na-compensated aluminosilicate JBW zeolite using experimental and computational techniques. The JBW framework, with Si/Al ratio of 1, is an ideal benchmark system as a stepping stone towards more complicated zeolites. The presence and mobility of water and extraframework species directly affect NMR fingerprints. Excellent agreement between theoretical and experimental spectra is obtained provided dynamic methods are employed with hydrated structural models. This work shows how NMR is instrumental in characterising aluminium distributions in zeolites at operating conditions.

Gold Open Access

DOI

https://doi.org/10.1002/chem.202202621

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Chemistry A European J - 2022 - Vanlommel - How Water and Ion Mobility Affect the NMR Fingerprints of the Hydrated JBW.pdf

Acidity effect on benzene methylation kinetics over substituted H-MeAlPO-5 catalysts

cnudde — Mon, 24 Jan 2022 08:51:50 +0000

M. Morten, T. Cordero-Lanzac, P. Cnudde, E. A. Redekop, S. Svelle, V. Van Speybroeck, U. Olsbye

Journal of Catalysis

404, 594-606

2021

Abstract

Methylation of aromatic compounds is a key reaction step in various industrial processes such as the aromatic cycle of methanol-to-hydrocarbons chemistry. The study of isolated methylation reactions and of the influence of catalyst acidity on their kinetics is a challenging task. Herein, we have studied unidirectional metal-substituted H-MeAlPO-5 materials to evaluate the effect of acid strength on the kinetics of benzene methylation with DME. First-principle simulations showed a direct correlation between the methylation barrier and acid site strength, which depends on the metal substituent. Three H-MeAlPO-5 catalysts with high (Me = Mg), moderate (Me = Si) and low acidity (Me = Zr) were experimentally tested, confirming a linear relationship between the methylation activation energy and acid strength. The effects of temperature and reactant partial pressure were evaluated, showing significant differences in the byproduct distribution between H-MgAlPO-5 and H-SAPO-5. Comparison with propene methylation suggested that the Mg substituted catalyst is also the most active for the selective methylation of alkenes.

Open Access version available at UGent repository

Gold Open Access

DOI

http://dx.doi.org/10.1016/j.jcat.2021.11.002

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Elucidation of the pre-nucleation phase directing metal-organic framework formation

leen — Tue, 07 Dec 2021 08:43:52 +0000

M. Filez, C. Caratelli, M. Rivera-Torrente, F. Muniz-Miranda, M. Hoek, M. Altelaar, A.J.R. Heck, V. Van Speybroeck, B.M. Weckhuysen

Cell Reports Physical Science

2, 12, 100680

2021

Abstract

Metal-organic framework (MOF) crystallization is governed by molecular assembly processes in the pre-nucleation stage. Yet, unravelling these pre-nucleation pathways and rationalizing their impact on crystal formation poses a great challenge since probing molecular-scale assemblies and macroscopic particles simultaneously is very complex. Herein, we present a multimodal, integrated approach to monitor MOF nucleation across multiple length scales by combining in situ optical spectroscopy, mass spectrometry, and molecular simulations. This approach allows tracing initial metal-organic complexes in solution and their assembly into oligomeric nuclei and simultaneously probing particle formation. During Co-ZIF-67 nucleation, a metal-organic pool forms with a variety of complexes caused by ligand exchange and symmetry reduction reactions. We discriminate complexes capable of initiating nucleation from growth species required for oligomerization into frameworks. Co4-nuclei are observed, which grow into particles following autocatalytic kinetics. The geometric and compositional variability of metal-organic pool species clarifies long-debated amorphous zeolitic imidazolate framework (ZIF)-particle nucleation and non-classic pathways of MOF crystallization.

DOI

dx.doi.org/10.1016/j.xcrp.2021.100680

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FengetalMatter2021.pdf

Mobility and Reactivity of Cu+ Species in Cu-CHA Catalysts under NH3-SCR-NOx Reaction Conditions: Insights from AIMD Simulations

cnudde — Fri, 17 Sep 2021 15:35:11 +0000

R. Millan, P. Cnudde, V. Van Speybroeck, M. Boronat

JACS Au (Journal of the American Chemical Society)

1 (10), 1778–1787

2021

Abstract

The mobility of the copper cations acting as active sites for the selective catalytic reduction of nitrogen oxides with ammonia in Cu-CHA catalysts varies with temperature and feed composition. Herein, the migration of [Cu(NH3)2]+ complexes between two adjacent cavities of the chabazite structure, including other reactant molecules (NO, O2, H2O, and NH3), in the initial and final cavities is investigated using ab initio molecular dynamics (AIMD) simulations combined with enhanced sampling techniques to describe hopping events from one cage to the other. We find that such diffusion is only significantly hindered by the presence of excess NH3 or NO in the initial cavity, since both reactants form with [Cu(NH3)2]+ stable intermediates which are too bulky to cross the 8-ring windows connecting the cavities. The presence of O2 modifies strongly the interaction of NO with Cu+. At low temperatures, we observe NO detachment from Cu+ and increased mobility of the [Cu(NH3)2]+ complex, while at high temperatures, NO reacts spontaneously with O2 to form NO2. The present simulations give evidence for recent experimental observations, namely, an NH3 inhibition effect on the SCR reaction at low temperatures, and transport limitations of NO and NH3 at high temperatures. Our first principle simulations mimicking operating conditions support the existence of two different reaction mechanisms operating at low and high temperatures, the former involving dimeric Cu(NH3)2-O2-Cu(NH3)2 species and the latter occurring by direct NO oxidation to NO2 in one single cavity.

Gold Open Access

DOI

http://dx.doi.org/10.1021/jacsau.1c00337

Interfacial study of clathrates confined in reversed silica pores

sven — Thu, 09 Sep 2021 09:03:10 +0000

P. M. Mileo, S.M.J. Rogge, M. Houlleberghs, E. Breynaert, J.A. Martens, V. Van Speybroeck

Journal of Materials Chemistry A

9(38), 21835-21844

2021

Abstract

Storing methane in clathrates is one of the most promising alternatives for transporting natural gas (NG) as it offers similar gas densities to liquefied and compressed NG while offering lower safety risks. However, the practical use of clathrates is limited given the extremely low temperatures and high pressures necessary to form these structures. Therefore, it has been suggested to confine clathrates in nanoporous materials, as this can facilitate clathrate's formation conditions while preserving its CH4 volumetric storage. Yet, the choice of nanoporous materials to be employed as the clathrate growing platform is still rather arbitrary. Herein, we tackle this challenge in a systematic way by computationally exploring the stability of clathrates confined in alkyl-grafted silica materials with different pore sizes, ligand densities and ligand types. Based on our findings, we are able to propose key design criteria for nanoporous materials favoring the stability of a neighbouring clathrate phase, namely large pore sizes, high ligand densities, and smooth pore walls. We hope that the atomistic insight provided in this work will guide and facilitate the development of new nanomaterials designed to promote the formation of clathrates.

Gold Open Access

DOI

http://dx.doi.org/10.1039/D1TA03105H

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Large-Scale Molecular Dynamics Simulations Reveal New Insights Into the Phase Transition Mechanisms in MIL-53(Al)

sven — Mon, 30 Aug 2021 07:57:29 +0000

S. Vandenhaute, S.M.J. Rogge, V. Van Speybroeck

Frontiers in Chemistry

9, 718920

2021

Abstract

Soft porous crystals have the ability to undergo large structural transformations upon exposure to external stimuli while maintaining their long-range structural order, and the size of the crystal plays an important role in this flexible behavior. Computational modeling has the potential to unravel mechanistic details of these phase transitions, provided that the models are representative for experimental crystal sizes and allow for spatially disordered phenomena to occur. Here, we take a major step forward and enable simulations of metal-organic frameworks containing more than a million atoms. This is achieved by exploiting the massive parallelism of state-of-the-art GPUs using the OpenMM software package, for which we developed a new pressure control algorithm that allows for fully anisotropic unit cell fluctuations. As a proof of concept, we study the transition mechanism in MIL-53(Al) under various external pressures. In the lower pressure regime, a layer-by-layer mechanism is observed, while at higher pressures, the transition is initiated at discrete nucleation points and temporarily induces various domains in both the open and closed pore phases. The presented workflow opens the possibility to deduce transition mechanism diagrams for soft porous crystals in terms of the crystal size and the strength of the external stimulus.

Gold Open Access

DOI

http://dx.doi.org/10.3389/fchem.2021.718920

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Crystals springing into action: metal-organic framework CUK-1 as a pressure-driven molecular spring dagger

louis — Tue, 18 May 2021 12:38:53 +0000

P. Iacomi, J.S. Lee, L. Vanduyfhuys, K. H. Cho, P. Fertey, J. Wieme, D. Granier, G. Maurin, V. Van Speybroeck, J.-S. Chang, P.G. Yot

Chemical Science

12, 5682-5687

2021

Abstract

Mercury porosimetry and in situ high pressure single crystal X-ray diffraction revealed the wine-rack CUK-1 MOF as a unique crystalline material capable of a fully reversible mechanical pressure-triggered structural contraction. The near-absence of hysteresis upon cycling exhibited by this robust MOF, akin to an ideal molecular spring, is associated with a constant work energy storage capacity of 40 J/gr. Molecular simulations were further deployed to uncover the free-energy landscape behind this unprecedented pressure-responsive phenomenon in the area of compliant hybrid porous materials. This discovery is of utmost importance from the perspective of instant energy storage and delivery.

Open Access version available at UGent repository

Green Open Access

DOI

http://dx.doi.org/10.1039/D1SC00205H

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