V. Van Speybroeck

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

Immobilization of Ir(I) complex on Covalent Triazine Frameworks for C-H Borylation Reactions: A Combined Experimental and Computational Study

N. Tahir, F. Muniz-Miranda, J. Everaert, P. Tack, T.S.A Heugebaert, K. Leus, L. Vincze, C. Stevens, V. Van Speybroeck, P. Van der Voort
Journal of Catalysis
371, 135-143
2019
A1

Abstract 

Metal-modified covalent triazine frameworks (CTFs) have attracted considerable attention in heterogeneous catalysis due to their strong nitrogen-metal interactions exhibiting superior activity, stability and hence recyclability. Herein, we report on a post-metalation of a bipyridine-based CTFs with an Ir(I) complex for CH borylation of aromatic compounds. Physical characterization of the Ir(I)-based bipyCTF catalyst in combination with density functional theory (DFT) calculations exhibit a high stabilization energy of the Ir-bipy moiety in the frameworks in the presence of B2Pin2. By using B2Pin2 as a boron source, Ir(I)@bipyCTF efficiently catalyzed the CH borylation of various aromatic compounds with excellent activity and good recyclability. In addition, XAS analysis of the Ir(I)@bipyCTF gave clear evidence for the coordination environment of the Ir.

DOI 

http://dx.doi.org/10.1016/j.jcat.2019.01.030

Active Role of Methanol in Post-Synthetic Linker Exchange in the Metal-Organic Framework UiO-66

J. Marreiros, C. Caratelli, J. Hajek, A. Krajnc, G. Fleury, B. Bueken, D. De Vos, G. Mali, M. Roeffaers, V. Van Speybroeck, R. Ameloot
Chemistry of Materials
31 (4), 1359-1369
2019
A1

Abstract 

UiO-66 is known as one of the most robust metal-organic framework materials. Nevertheless, UiO-66 has also been shown to undergo post-synthetic exchange of structural linkers with surprising ease in some sol-vents. To date the exchange mechanism has not yet been fully elucidated. Here, we show how time-resolved monitoring grants insight into the selected case of exchanging 2-aminoterephthalic acid into UiO-66 in methanol. Analysis of both the solid and liquid phase, complemented by computational insights, revealed the active role of methanol in the creation and stabilization of metastable states in which dangling linkers are similar to monocarboxylate defects that can be introduced during UiO-66 synthesis, such dangling link-ers undergo fast exchange. The presence of missing linker or missing cluster defects at the start of the ex-change process was shown to have no considerable impact on the equilibrium composition. After the ex-change process, the incoming 2-aminoterephthalate and remaining terephthalate linkers were distributed homogeneously in the framework for the typical small crystal size of UiO-66 (≈500nm).

Open Access version available at UGent repository
Green Open Access

DOI 

http://dx.doi.org/10.1021/acs.chemmater.8b04734

Ab initio evaluation of Henry coefficients using importance sampling

S. Vandenbrande, M. Waroquier, V. Van Speybroeck, T. Verstraelen
Journal of Chemical Theory and Computation
14 (12), 6359–6369
2018
A1

Abstract 

We present a new algorithm that allows for an efficient evaluation of the Henry coefficient of a guest molecule inside a porous material, which permits to use ab initio energy calculations. The Widom insertion method, which is currently used to compute these Henry coefficients, typically requires millions of energy evaluations. Our new methodology reduces this number by more than 1 order of magnitude, enabling the use of an ab initio potential energy surface. The methodology we propose is reminiscent of the well-known importance sampling technique which is frequently used in Monte Carlo integrations. First, a conventional Widom insertion simulation is performed using a force field. In the second step, the Widom results are used to select a limited number of configurations and only for these configurations the ab initio evaluation of the energy is required. Finally, by appropriately reweighting the latter energies, an accurate estimation of the ab initio Henry coefficient is possible at a moderate computational cost. We apply our methodology to the adsorption of CO2 in Mg-MOF-74, a prototypical case where interactions of a polar guest molecule with unsaturated metal sites dominate the adsorption mechanism. In this case generic force fields such as UFF or Dreiding are inappropriate and the use of ab initio methods is indispensable. In a second case study, we compute Henry coefficients of methane in UiO-66 using different levels of theory. We pay particular attention to the influence of the dispersion corrections and the role of many-body effects. For the final example, we qualitatively investigate adsorption features for a series of functionalized UiO-66 frameworks. Overall the cases we present show that accurate computations of Henry coefficients is extremely challenging, as different levels of theory provide strongly varying results. At the same time ab initio calculations have added value compared to force fields, as they provide a physically more sound description of the adsorption mechanism and in some cases clearly improve correspondence with experiment.

Open Access version available at UGent repository
Gold Open Access

DOI 

http://dx.doi.org/10.1021/acs.jctc.8b00892

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

Structure–performance descriptors and the role of Lewis acidity in the methanol-to-propylene process

I. Yarulina, K. De Wispelaere, S. Bailleul, J. Goetze, M. Radersma, E. Abou-Hamad, I. Vollmer, M. Goesten, B. Mezari, E.J.M. Hensen, J. S. Martínez-Espín, M. Morten, S. Mitchell, J. Perez-Ramirez, U. Olsbye, B.M. Weckhuysen, V. Van Speybroeck, F. Kapteijn, J. Gascon
Nature Chemistry
10 (8), 804-812
2018
A1

Abstract 

The combination of well-defined acid sites, shape-selective properties and outstanding stability places zeolites among the most practically relevant heterogeneous catalysts. The development of structure–performance descriptors for processes that they catalyse has been a matter of intense debate, both in industry and academia, and the direct conversion of methanol to olefins is a prototypical system in which various catalytic functions contribute to the overall performance. Propylene selectivity and resistance to coking are the two most important parameters in developing new methanol-to-olefin catalysts. Here, we present a systematic investigation on the effect of acidity on the performance of the zeolite ‘ZSM-5’ for the production of propylene. Our results demonstrate that the isolation of Brønsted acid sites is key to the selective formation of propylene. Also, the introduction of Lewis acid sites prevents the formation of coke, hence drastically increasing catalyst lifetime.

DOI 

http://dx.doi.org/10.1038/s41557-018-0081-0

i-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations

V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng, A. Cuzzocrea, R.H. Meißner, D. Wilkins, P. Juda, S.P. Bienvenue, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf, T. Kühne, D. Manolopoulos, T. Markland, J. Richardson, A. Tkatchenko, G.A. Tribello, V. Van Speybroeck, M. Ceriotti
Computer Physics Communications
236, 214-223
2019
A1

Abstract 

Progress in the atomic-scale modelling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born-Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives.

http://arxiv.org/abs/1808.03824

Open Access version available at UGent repository
Green Open Access

DOI 

http://dx.doi.org/10.1016/j.cpc.2018.09.020

Use of 3-Hydroxy-4-(trifluoromethyl)azetidin-2-ones as Building Blocks for the Preparation of Trifluoromethyl-Containing Aminopropanes, 1,3-Oxazinan-2-ones, Aziridines, and 1,4-Dioxan-2-ones

H.D. Thi, G. Le Nhat Thuy, S. Catak, V. Van Speybroeck, T. Van Nguyen, M. D'Hooghe
Synthesis-Stuttgart
50, 1439-1456
2018
A1

Abstract 

3-Hydroxy- 4-(trifluoromethyl)azetidin- 2-ones were efficiently synthesized from the corresponding 3-benzyloxy-β-lactams and successfully transformed into 3-chloro- 4-(trifluoromethyl)azetidin-2- one building blocks. The latter chlorides were shown to be eligible precursors for the construction of novel CF 3 -containing aminopropanes, 1,3-oxazinanes, 1,3-oxazinan-2- ones and aziridines. In addition, 3-hydroxy- 4-(trifluoromethyl)azetidin- 2-ones proved to be interesting substrates for the synthesis of novel 3-[2,2,2- trifluoro-1-(arylamino)ethyl]-1,4- dioxan-2- ones via intramolecular cyclization of 3-(2- hydroxyethoxy)-β-lactam intermediates.

DOI 

http://dx.doi.org/10.1055/s-0036-1591537

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