Center for Molecular Modeling - IAP VII P7/05 B/12909/*

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

jelle — Fri, 21 Dec 2018 13:23:48 +0000

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

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

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paper_ZKrist.pdf

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

ruben — Thu, 02 Aug 2018 14:01:16 +0000

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

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

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acs.jctc_.8b00725.pdf

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

wim — Tue, 26 Jun 2018 06:37:22 +0000

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

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

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s41557-018-0081-0.pdf

Tuning the balance between dispersion and entropy to design temperature-responsive flexible metal-organic frameworks

kurt — Fri, 23 Feb 2018 19:44:00 +0000

J. Wieme, K. Lejaeghere, G. Kresse, V. Van Speybroeck

Nature Communications

9, 4899

2018

DOI

http://dx.doi.org/10.1038/s41467-018-07298-4

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Wieme_2018_NatureCommun_dispersion-vs-entropy-MIL53.pdf

Theoretical Insight into the Regioselective Ring-Expansions of Bicyclic Aziridinium Ions

wim — Mon, 11 Dec 2017 07:55:05 +0000

E. Birsen Boydas, G. Tanriver, M. D'Hooghe, H-J. Ha, V. Van Speybroeck, S. Catak

Organic & Biomolecular Chemistry

16 (5), 796-806

2018

Abstract

Transient bicyclic aziridinium ions are known to undergo ring-expansion reactions, paving the way to functionalized nitrogen-containing heterocycles. In this study, the regioselectivity observed in the ring-expansion reactions of 1-azoniabicyclo[n.1.0]alkanes was investigated from a computational viewpoint to study the ring-expansion pathways of two bicyclic systems with different ring sizes. Moreover, several nucleophiles leading to different experimental results were investigated. The effect of solvation was taken into account using both explicit and implicit solvent models. This theoretical rationalization provides valuable insight into the observed regioselectivity and may be used as a predictive tool in future studies.

DOI

http://dx.doi.org/10.1039/C7OB02253K

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OBC-revised.pdf

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

chiara — Wed, 06 Dec 2017 09:54:36 +0000

J. Hajek, C. Caratelli, R. Demuynck, K. De Wispelaere, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck

Chemical Science

9 (10), 2723-2732

2018

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

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c7sc04947a.pdf

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

wim — Mon, 27 Nov 2017 07:12:54 +0000

L. Vanduyfhuys, S. Vandenbrande, J. Wieme, M. Waroquier, T. Verstraelen, V. Van Speybroeck

Journal of Computational Chemistry

39 (16), p. 999-1011

2018

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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published_online.pdf

Thermodynamic insight into stimuli-responsive behavior of soft porous crystals

michel — Sat, 11 Nov 2017 15:22:43 +0000

L. Vanduyfhuys, S.M.J. Rogge, J. Wieme, S. Vandenbrande, G. Maurin, M. Waroquier, V. Van Speybroeck

Nature Communications

9, 1, 204

2018

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

DOI

http://dx.doi.org/10.1038/s41467-017-02666-y

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published.pdf

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

michel — Sat, 11 Nov 2017 15:06:22 +0000

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

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).

DOI

http://dx.doi.org/10.1021/acs.jctc.7b01134

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

alexander — Wed, 08 Nov 2017 12:46:42 +0000

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

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

DOI

http://dx.doi.org/10.1021/acs.jpcc.7b11031

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published.pdf