S.M.J. Rogge

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.

Thermodynamic insight into stimuli-responsive behavior of soft porous crystals

L. Vanduyfhuys, S.M.J. Rogge, J. Wieme, S. Vandenbrande, G. Maurin, M. Waroquier, V. Van Speybroeck
Nature Communications
9, 1, 204
2018
A1

Abstract 

Knowledge of the thermodynamic potential in terms of the independent variables allows to characterize the macroscopic state of the system. However, in practice, it is difficult to access this potential experimentally due to irreversible transitions that occur between equilibrium states. A showcase example of sudden transitions between (meta)stable equilibrium states is observed for soft porous crystals possessing a network with long-range structural order, which can transform between various states upon external stimuli such as pressure, temperature and guest adsorption. Such phase transformations are typically characterized by large volume changes and may be followed experimentally by monitoring the volume change in terms of certain external triggers. Herein, we present a generalized thermodynamic approach to construct the underlying Helmholtz free energy as a function of the state variables that governs the observed behaviour based on microscopic simulations. This concept allows a unique identification of the conditions under which a material becomes flexible.

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).

Elucidating the Vibrational Fingerprint of the Flexible Metal-Organic Framework MIL-53(Al) Using a Combined Experimental/Computational Approach

A.E.J. Hoffman, L. Vanduyfhuys, I. Nevjestic, J. Wieme, S.M.J. Rogge, H. Depauw, P. Van der Voort, H. Vrielinck, V. Van Speybroeck
Journal of Physical Chemistry C
122, 5, 2734-2746
2018
A1

Abstract 

In this work mid-infrared (mid-IR), far-IR, and Raman spectra are presented for the distinct (meta)stable phases of the flexible metal-organic framework MIL-53(Al). Static density functional theory (DFT) simulations are performed allowing for the identification of all IR active modes, which is unprecedented in the low-frequency region. A unique vibrational fingerprint is revealed, resulting from aluminum-oxide backbone stretching modes, which can be used to clearly distinguish the IR spectra of the closed- and large-pore phases. Furthermore, molecular dynamics simulations based on a DFT description of the potential energy surface enable to determine the theoretical Raman spectrum of the closed- and large-pore phases for the first time. An excellent correspondence between theory and experiment is observed. Both the low-frequency IR and Raman spectra show major differences in vibrational modes between the closed- and large-pore phases indicating changes in lattice dynamics between the two structures. In addition, several collective modes related to the breathing mechanism in MIL-53(Al) are identified. In particular, we rationalize the importance of the trampoline-like motion of the linker for the phase transition.

Open Access version available at UGent repository
Gold Open Access

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

Reliably Modeling the Mechanical Stability of Rigid and Flexible Metal-Organic Frameworks

S.M.J. Rogge, M. Waroquier, V. Van Speybroeck
Accounts of Chemical Research
51 (1), 138-148
2018
A1

Abstract 

Over the past two decades, metal–organic frameworks (MOFs) have matured from interesting academic peculiarities toward a continuously expanding class of hybrid, nanoporous materials tuned for targeted technological applications such as gas storage and heterogeneous catalysis. These oft-times crystalline materials, composed of inorganic moieties interconnected by organic ligands, can be endowed with desired structural and chemical features by judiciously functionalizing or substituting these building blocks. As a result of this reticular synthesis, MOF research is situated at the intriguing intersection between chemistry and physics, and the building block approach could pave the way toward the construction of an almost infinite number of possible crystalline structures, provided that they exhibit stability under the desired operational conditions. However, this enormous potential is largely untapped to date, as MOFs have not yet found a major breakthrough in technological applications. One of the remaining challenges for this scale-up is the densification of MOF powders, which is generally achieved by subjecting the material to a pressurization step. However, application of an external pressure may substantially alter the chemical and physical properties of the material. A reliable theoretical guidance that can presynthetically identify the most stable materials could help overcome this technological challenge.

In this Account, we describe the recent research the progress on computational characterization of the mechanical stability of MOFs. So far, three complementary approaches have been proposed, focusing on different aspects of mechanical stability: (i) the Born stability criteria, (ii) the anisotropy in mechanical moduli such as the Young and shear moduli, and (iii) the pressure-versus-volume equations of state. As these three methods are grounded in distinct computational approaches, it is expected that their accuracy and efficiency will vary. To date, however, it is unclear which set of properties are suited and reliable for a given application, as a comprehensive comparison for a broad variety of MOFs is absent, impeding the widespread use of these theoretical frameworks.

Herein, we fill this gap by critically assessing the performance of the three computational models on a broad set of MOFs that are representative for current applications. These materials encompass the mechanically rigid UiO-66(Zr) and MOF-5(Zn) as well as the flexible MIL-47(V) and MIL-53(Al), which undergo pressure-induced phase transitions. It is observed that the Born stability criteria and pressure-versus-volume equations of state give complementary insight into the macroscopic and microscopic origins of instability, respectively. However, interpretation of the Born stability criteria becomes increasingly difficult when less symmetric materials are considered. Moreover, pressure fluctuations during the simulations hamper their accuracy for flexible materials. In contrast, the pressure-versus-volume equations of state are determined in a thermodynamic ensemble specifically targeted to mitigate the effects of these instantaneous fluctuations, yielding more accurate results. The critical Account presented here paves the way toward a solid computational framework for an extensive presynthetic screening of MOFs to select those that are mechanically stable and can be postsynthetically densified before their use in targeted applications.

Open Access version available at UGent repository
Gold Open Access

Influence of a confined methanol solvent on the reactivity of active sites in UiO-66

C. Caratelli, J. Hajek, S.M.J. Rogge, S. Vandenbrande, E.J. Meijer, M. Waroquier, V. Van Speybroeck
ChemPhysChem
19 (4), 420-429
2018
A1

Abstract 

UiO-66, composed of Zr-oxide bricks and terephthalate linkers, is currently one of the most studied metal-organic frameworks due to its exceptional stability. Defects can be introduced in the structure, creating undercoordinated Zr atoms which are Lewis acid sites. Here, additional Brønsted sites can be generated by coordinated protic species from the solvent. In this contribution, a multilevel modeling approach was applied to unravel the effect of a confined methanol solvent on the active sites in UiO-66. First, active sites were explored with static periodic density functional theory calculations to investigate adsorption of water and methanol. Solvent was then introduced in the pores with grand canonical Monte Carlo simulations, followed by a series of molecular dynamics simulations at operating conditions. A hydrogen-bonded network of methanol molecules is formed, allowing the protons to shuttle between solvent methanol, adsorbed water, and the inorganic brick. Upon deprotonation of an active site, the methanol solvent aids the transfer of protons and stabilizes charged configurations via hydrogen bonding, which could be crucial in stabilizing reactive intermediates. The multilevel modeling approach adopted here sheds light on the important role of a confined solvent on the active sites in the UiO-66 material, introducing dynamic acidity in the system at finite temperatures by which protons may be easily shuttled from various positions at the active sites.

Open Access version available at UGent repository
Gold Open Access

Metal-organic and covalent organic frameworks as single-site catalysts

S.M.J. Rogge, A. Bavykina, J. Hajek, H. Garcia, A.I. Olivos-Suarez, A. Sepúlveda-Escribano, A. Vimont, G. Clet, P. Bazin, F. Kapteijn, M. Daturi, E.V. Ramos-Fernandez, F.X. Llabres i Xamena, V. Van Speybroeck, J. Gascon
Chemical Society Reviews
46 (11), 3134-3184
2017
A1

Abstract 

Heterogeneous single-site catalysts consist of isolated, well-defined, active sites that are spatially separated in a given solid and, ideally, structurally identical. In this review, the potential of metal–organic frameworks (MOFs) and covalent organic frameworks (COFs) as platforms for the development of heterogeneous single-site catalysts is reviewed thoroughly. In the first part of this article, synthetic strategies and progress in the implementation of such sites in these two classes of materials are discussed. Because these solids are excellent playgrounds to allow a better understanding of catalytic functions, we highlight the most important recent advances in the modelling and spectroscopic characterization of single-site catalysts based on these materials. Finally, we discuss the potential of MOFs as materials in which several single-site catalytic functions can be combined within one framework along with their potential as powerful enzyme-mimicking materials. The review is wrapped up with our personal vision on future research directions.

Open Access version available at UGent repository
Gold Open Access

Thermodynamic Insight in the High-Pressure Behavior of UiO-66: Effect of Linker Defects and Linker Expansion

S.M.J. Rogge, J. Wieme, L. Vanduyfhuys, S. Vandenbrande, G. Maurin, T. Verstraelen, M. Waroquier, V. Van Speybroeck
Chemistry of Materials
28 (16), 5721-5732
2016
A1

Abstract 

In this Article, we present a molecular-level understanding of the experimentally observed loss of crystallinity in UiO-66-type metal–organic frameworks, including the pristine UiO-66 to -68 as well as defect-containing UiO-66 materials, under the influence of external pressure. This goal is achieved by constructing pressure-versus-volume profiles at finite temperatures using a thermodynamic approach relying on ab initio derived force fields. On the atomic level, the phenomenon is reflected in a sudden drop in the number of symmetry operators for the crystallographic unit cell because of the disordered displacement of the organic linkers with respect to the inorganic bricks. For the defect-containing samples, a reduced mechanical stability is observed, however, critically depending on the distribution of these defects throughout the material, hence demonstrating the importance of judiciously characterizing defects in these materials.

This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.
http://pubs.acs.org/doi/abs/10.1021/acs.chemmater.6b01956

Open Access version available at UGent repository
Gold Open Access

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