L. Vanduyfhuys

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
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.

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

QuickFF: toward a generally applicable methodology to quickly derive accurate 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
2015
A1
Published while none of the authors were employed at the CMM

Metal-organic frameworks as potential shock absorbers: the case of the highly flexible MIL-53(Al)

P.G. Yot, Z. Boudene, J. Macia, D. Granier, L. Vanduyfhuys, T. Verstraelen, V. Van Speybroeck, T. Devic, C. Serre, G. Ferey, N. Stock, G. Maurin
Chemical Communications
50, 9462-9464
2014
A1

Abstract 

The mechanical energy absorption ability of the highly flexible; MIL-53(Al) MOF material was explored using a combination of; experiments and molecular simulations. A pressure-induced transition; between the large pore and the closed pore forms of this solid; was revealed to be irreversible and associated with a relatively large; energy absorption capacity. Both features make MIL-53(Al) the first; potential MOF candidate for further use as a shock absorber.

Open Access version available at UGent repository

On the thermodynamics of framework breathing: A free energy model for gas adsorption in MIL-53

A. Ghysels, L. Vanduyfhuys, M. Vandichel, M. Waroquier, V. Van Speybroeck, B. Smit
Journal of Physical Chemistry C
117, 11540-11554
2013
A1

Abstract 

When adsorbing guest molecules, the porous metal-organic framework MIL-53(Cr) may vary its cell parameters drastically while retaining its crystallinity. A first approach to the thermodynamic analysis of this 'framework breathing' consists of comparing the osmotic potential in two distinct shapes only (large-pore and narrow-pore). In this paper, we propose a generic parametrized free energy model including three contributions: host free energy, guest-guest interactions, and host-guest interaction. Free energy landscapes may now be constructed scanning all shapes and any adsorbed amount of guest molecules. This allows to determine which shapes are the most stable states for arbitrary combinations of experimental control parameters, such as the adsorbing gas chemical potential, the external pressure, and the temperature. The new model correctly reproduces the structural transitions along the CO2 and CH4 isotherms. Moreover, our model successfully explains the adsorption versus desorption hysteresis as a consequence of the creation, stabilization, destabilization, and disappearance of a second free energy minimum under the assumptions of a first order phase transition and collective behavior. Our general thermodynamic description allows to decouple the gas chemical potential μ and mechanical pressure P as two independent thermodynamic variables and predict the complete (μ,P) phase diagram for CO2 adsorption in MIL-53(Cr). The free energy model proposed here is an important step towards a general thermodynamics description of flexible metal-organic frameworks.

Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol

M. Van Houteghem, T. Verstraelen, A. Ghysels, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck
Journal of Chemical Physics
137 (10), 104506
2012
A1

Abstract 

An ecient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in dierent molecules and was calibrated by tting reference BSSE data points computed with the counterpoise method. It is veried that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e. methanol, and more specic on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.

Open Access version available at UGent repository

Ab initio parametrized force field for the flexible metal-organic framework MIL-53(Al)

L. Vanduyfhuys, T. Verstraelen, M. Vandichel, M. Waroquier, V. Van Speybroeck
Journal of Chemical Theory and Computation (JCTC)
8 (9), 3217-3231
2012
A1

Abstract 

A force field is proposed for the flexible metal-organic framework MIL-53(Al), which is calibrated using density functional theory calculations on non-periodic clusters. The force field has three main contributions: an electrostatic term based on atomic charges derived with a modified Hirshfeld-I method, a van der Waals (vdW) term with parameters taken from the MM3 model and a valence force field whose parameters were estimated with a new methodology that uses the gradients and Hessian matrix elements retrieved from non-periodic cluster calculations. The new force field, predicts geometries and cell parameters that compare well with the experimental values both for the large and narrow pore phases. The energy profile along the breathing mode of the empty material reveals the existence of two minima, which confirms the intrinsic bistable behaviour of the MIL-53. Even without the stimulus of external guest molecules the material may transform from the large pore (lp) to the narrow pore (np) phase [Liu et al. JACS 2008, 120, 11813]. The relative stability of the two phases critically depends on the vdW parameters and MM3 dispersion interaction has the tendency to overstabilize the np phase.

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