L. Vanduyfhuys

Exploring the flexibility of MIL-47(V)-type materials using force field molecular dynamics simulations

J. Wieme, L. Vanduyfhuys, S.M.J. Rogge, M. Waroquier, V. Van Speybroeck
Journal of Physical Chemistry C
120 (27), 14934-14947
2016
A1

Abstract 

The flexibility of three MIL-47(V)-type materials (MIL-47, COMOC-2 and COMOC-3) has been explored by constructing the pressure-versus-volume and free energy-versus-volume curves at various temperatures ranging from 100 K to 400 K. This is done with first-principles based force fields using the recently proposed QuickFF parameterization protocol. Specific terms were added for the materials at hand to describe the asymmetry of the one-dimensional vanadium-oxide chain and to account for the flexibility of the organic linkers. The force fields are used in a series of molecular dynamics simulations at fixed volumes, but varying unit cell shapes. The three materials show a distinct pressure-versus-volume behavior, which underlines the ability to tune the mechanical properties by varying the linkers towards different applications such as nanosprings, dampers and shock absorbers.

Open Access version available at UGent repository

DOI 

http://dx.doi.org/10.1021/acs.jpcc.6b04422

A breathing zirconium metal-organic framework with reversible loss of crystallinity by correlated nanodomain formation

B. Bueken, F. Vermoortele, M.J. Cliffe, M.T. Wharmby, D. Foucher, J. Wieme, L. Vanduyfhuys, C. Martineau, N. Stock, F. Taulelle, V. Van Speybroeck, A.L. Goodwin, D. De Vos
Chemistry - A European Journal
2016, 22, 1-5
2016
A1

Abstract 

The isoreticular analogue of the metal–organic framework UiO-66(Zr), synthesized with the flexible trans-1,4-cyclohexanedicarboxylic acid as linker, shows a peculiar breathing behavior by reversibly losing long-range crystalline order upon evacuation. The underlying flexibility is attributed to a concerted conformational contraction of up to two thirds of the linkers, which breaks the local lattice symmetry. X-ray scattering data are described well by a nanodomain model in which differently oriented tetragonal-type distortions propagate over about 7–10 unit cells.

DOI 

http://dx.doi.org/10.1002/chem.201600330

Is the error on first-principles volume predictions absolute or relative?

K. Lejaeghere, L. Vanduyfhuys, T. Verstraelen, V. Van Speybroeck, S. Cottenier
Computational Materials Science
117, 390-396
2016
A1

Abstract 

Many benchmarks of density-functional theory with respect to experiment suggest the error on predicted equilibrium volumes to scale with the volume. Relative volume errors are therefore often used as a decisive argument to select one exchange-correlation functional over another. We show that the error on the volume (after correcting for systematic deviations) is only approximately relative. A simple analytic model, validated by rigorous Monte Carlo simulations, reveals that a more accurate error estimate can be derived from the inverse of the bulk modulus. This insight is not only instrumental for the selection or design of suitable functionals. It also calls for a new attitude towards computational errors: to report computational errors on electronic-structure calculations, identify systematic deviations and distinguish between relative and absolute effects. (C) 2016 Elsevier B.V. All rights reserved.

Open Access version available at UGent repository

DOI 

http://dx.doi.org/10.1016/j.commatsci.2016.01.039

Vibrational fingerprint of the absorption properties of UiO-type MOF materials

A. Van Yperen-De Deyne, K. Hendrickx, L. Vanduyfhuys, G. Sastre, P. Van der Voort, V. Van Speybroeck, K. Hemelsoet
Theoretical Chemistry Accounts
135, 4, 102
2016
A1

Abstract 

The absorption properties of UiO-type metal–organic frameworks are computed using TD-DFT simulations on the organic linkers. A set of nine isoreticular structures, including the UiO-66 and UiO-67 materials and functionalized variants, are examined. The excitation energies from a static geometry optimization are compared with dynamic averages obtained from sampling the ground-state potential energy surface using molecular dynamics. The vibrational modes that impact the excitation energy are identified. This analysis is done using a recently proposed tool based on power spectra of the velocities and the excitation energies. The applied procedure allows including important factors influencing the absorption spectra, such as the periodic framework, linker variation and dynamical effects including harmonic and anharmonic nuclear motions. This methodology allows investigating in detail the vibrational fingerprint of the excitation energy of advanced materials such as MOFs and gives perspectives to tailor materials toward new light-based applications.

Open Access version available at UGent repository

DOI 

http://dx.doi.org/10.1007/s00214-016-1842-8

Mechanical energy storage performance of an aluminum fumarate metal-organic framework

P.G. Yot, L. Vanduyfhuys, E. Alvarez, J. Rodriguez, J.-P. Itié, P. Fabry, N. Guillou, T. Devic, P.L. Llewellyn, V. Van Speybroeck, C. Serre, G. Maurin
Chemical Science
7, 446-450
2016
A1

Abstract 

The aluminum fumarate MOF A520 or MIL-53-FA is revealed to be a promising material for mechanical energy-related applications with performances in terms of work and heat energies which surpass those of any porous solids reported so far. Complementary experimental and computational tools are deployed to finely characterize and understand the pressure-induced structural transition at the origin of these unprecedented levels of performance.

Open Access version available at UGent repository

DOI 

http://dx.doi.org/10.1039/C5SC02794B

A comparison of barostats for the mechanical characterization of metal-organic frameworks

S.M.J. Rogge, L. Vanduyfhuys, A. Ghysels, M. Waroquier, T. Verstraelen, G. Maurin, V. Van Speybroeck
Journal of Chemical Theory and Computation (JCTC)
11 (12), 5583-5597
2015
A1

Abstract 

In this paper, three barostat coupling schemes for pressure control, which are commonly used in molecular dynamics simulations, are critically compared to characterise the rigid MOF-5 and the flexible MIL-53(Al) metal-organic frameworks. We investigate the performance of the three barostats, the Berendsen, the Martyna-Tuckerman-Tobias-Klein (MTTK) and the Langevin coupling methods, in reproducing the cell parameters and the pressure versus volume behaviour in isothermal-isobaric simulations. A thermodynamic integration method is used to construct the free energy profiles as a function of volume at finite temperature. It is observed that the aforementioned static properties are well reproduced with the three barostats. However, for static properties depending nonlinearly on the pressure, the Berendsen barostat might give deviating results as it suppresses pressure fluctuations more drastically. Finally, dynamic properties, which are directly related to the fluctuations of the cell, such as the time to transition from the large-pore to the closed-pore phase, cannot be well reproduced by any of the coupling schemes.

DOI 

http://dx.doi.org/10.1021/acs.jctc.5b00748

Fine-tuning the theoretically predicted structure of MIL-47(V) with the aid of powder X-ray diffraction

T. Bogaerts, L. Vanduyfhuys, D.E.P. Vanpoucke, J. Wieme, M. Waroquier, P. Van der Voort, V. Van Speybroeck
CrystEngComm
17, 8612–8622
2015
A1

Abstract 

The structural characterization of complex crystalline materials such as metal organic frameworks can prove a very difficult challenge both for experimentalists as for theoreticians. From theory, the flat potential energy surface of these highly flexible structures often leads to different geometries that are energetically very close to each other. In this work a distinction between various computationally determined structures is made by comparing experimental and theoretically derived X-ray diffractograms which are produced from the materials geometry. The presented approach allows to choose the most appropriate geometry of a MIL-47(V) MOF and even distinguish between different electronic configurations that induce small structural changes. Moreover the techniques presented here are used to verify the applicability of a newly developed force field for this material. The discussed methodology is of significant importance for modelling studies where accurate geometries are crucial, such as mechanical properties and adsorption of guest molecules.

DOI 

http://dx.doi.org/10.1039/C5CE01388G

On the stability and nature of adsorbed pentene in Brønsted acid zeolite H-ZSM-5 at 323 K

J. Hajek, J. Van der Mynsbrugge, K. De Wispelaere, P. Cnudde, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck
Journal of Catalysis
340, 227 - 235
2016
A1

Abstract 

Adsorption of linear pentenes in H-ZSM-5 at 323 K is investigated using contemporary static and molecular dynamics methods. A physisorbed complex corresponding to free pentene, a π-complex and a chemisorbed species may occur. The chemisorbed species can be either a covalently bonded alkoxide or an ion pair, the so-called carbenium ion. Without finite temperature effects, the π-complex is systematically slightly more bound than the chemisorbed alkoxide complex, whereas molecular dynamics calculations at 323 K yield an almost equal stability of both species. The carbenium ion was not observed during simulations at 323 K. The transformation from the π-complex to the chemisorbed complex is activated by a free energy in the range of 33–42 kJ/mol. Our observations yield unprecedented insights into the stability of elusive intermediates in zeolite catalysis, for which experimental data are very hard to measure.

Open Access version available at UGent repository

DOI 

http://dx.doi.org/10.1016/j.jcat.2016.05.018

Semi-Analytical mean-field model for predicting breathing in Metal-Organic Frameworks

L. Vanduyfhuys, A. Ghysels, S.M.J. Rogge, R. Demuynck, V. Van Speybroeck
Molecular Simulation
41, 16-17, 1311-1328
2015
A1

Abstract 

A new semi-analytical model is proposed to rationalize breathing of MIL-53 type materials. The model is applied on two case studies, the guest-induced breathing of MIL-53(Cr) with CO 2 and CH 4 , and the phase transformations for MIL-53(Al) upon xenon adsorption. Experimentally, MIL-53(Cr) breathes upon CO 2 adsorption, which was not observed for CH 4 . This result could be ascribed to the stronger interaction of carbon dioxide with the host matrix. For MIL-53(Al) a phase transition from the large pore phase could be enforced to an intermediate phase with volumes of about 1160 − 1300 A, which corresponds well to the phase observed experimentally upon xenon adsorption. Our thermodynamic model correlates nicely with the adsorption pressure model proposed by Coudert et al. Furthermore the model can predict breathing behavior of other flexible materials, if the user can determine the free energy of the empty host, the interaction energy between a guest molecule and the host matrix and the pore volume accessible to the guest molecules. This will allow to generate the osmotic potential from which the equilibria can be deduced and the anticipated experimentally observed phase may be predicted.

Open Access version available at UGent repository

DOI 

http://dx.doi.org/10.1080/08927022.2015.1048512

QuickFF: A program for a quick and easy derivation of force fields for Metal-Organic Frameworks from ab initio input

L. Vanduyfhuys, S. Vandenbrande, T. Verstraelen, R. Schmid, M. Waroquier, V. Van Speybroeck
Journal of Computational Chemistry
36, 13, 1015–1027
2015
A1

Abstract 

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort.

Open Access version available at UGent repository

DOI 

http://dx.doi.org/10.1002/jcc.23877

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