V. Van Speybroeck

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.

Mechanical properties from periodic plane wave QM codes: the challenge of the flexible nanoporous MIL-47 (V) framework

D.E.P. Vanpoucke, K. Lejaeghere, V. Van Speybroeck, M. Waroquier, A. Ghysels
Journal of Physical Chemistry C
119, 23752-23766
2015
A1

Abstract 

Modeling the flexibility of metal–organic frameworks (MOFs) requires the computation of mechanical properties from first principles, e.g., for screening of materials in a database, for gaining insight into structural transformations, and for force field development. However, this paper shows that computations with periodic density functional theory are challenged by the flexibility of these materials: guidelines from experience with standard solid-state calculations cannot be simply transferred to flexible porous frameworks. Our test case, the MIL-47(V) material, has a large-pore and a narrow-pore shape. The effect of Pulay stress (cf. Pulay forces) leads to drastic errors for a simple structure optimization of the flexible MIL-47(V) material. Pulay stress is an artificial stress that tends to lower the volume and is caused by the finite size of the plane wave basis set. We have investigated the importance of this Pulay stress, of symmetry breaking, and of k-point sampling on (a) the structure optimization and (b) mechanical properties such as elastic constants and bulk modulus, of both the large-pore and narrow-pore structure of MIL-47(V). We found that, in the structure optimization, Pulay effects should be avoided by using a fitting procedure, in which an equation of state E(V) (EOS) is fit to a series of energy versus volume points. Manual symmetry breaking could successfully lower the energy of MIL-47(V) by distorting the vanadium–oxide distances in the vanadyl chains and by rotating the benzene linkers. For the mechanical properties, the curvature of the EOS curve was compared with the Reuss bulk modulus, derived from the elastic tensor in the harmonic approximation. Errors induced by anharmonicity, the eggbox effect, and Pulay effects propagate into the Reuss modulus. The strong coupling of the unit cell axes when the unit cell deforms expresses itself in numerical instability of the Reuss modulus. For a flexible material, it is therefore advisible to resort to the EOS fit procedure.

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.

Mechanistic studies of aldol condensations in UiO-66 and UiO-66-NH2

J. Hajek, M. Vandichel, B. Van de Voorde, B. Bueken, D. De Vos, M. Waroquier, V. Van Speybroeck
Journal of Catalysis
331, 1-12
2015
A1

Abstract 

A full mechanistic investigation is proposed for the industrially important cross-aldol condensation reaction of heptanal with benzaldehyde on the UiO-66 and the amino-functionalized UiO-66-NH2 metal–organic frameworks to form jasminaldehyde. Several experimental studies indicate that the activity for the aldol condensation reaction can be increased by proper functionalization of the material, e.g. by introducing an additional basic amino site and thus creating a bifunctional acid–base catalyst for the aldol condensation. The precise molecular level origin for this behavior is to date unclear. Herein state-of-the-art Density-Functional Theory (DFT) calculations have been performed to unravel the mechanism of the cross- and self-aldol condensations of benzaldehyde and propanal. To this end free energy calculations have been performed on both extended cluster and periodic models. It is found that the mechanism on both catalysts is essentially the same, although a slightly stronger adsorption of the reactants and slightly lower barriers were found on the amino functionalized material, pointing toward higher initial activities. New experiments were performed to confirm these observations. It is indeed found that the initial activity toward cross-aldol condensation on the amino functionalized material is higher, although after about 40 min of reaction both materials become equally active. Our results furthermore point out that the basic amino groups may promote side reactions such as imine formation, which is induced by water. The study as presented can assist to engineer materials at the molecular level toward the desired products.

Open Access version available at UGent repository

Shape-selective diffusion of olefins in 8-ring solid acid microporous zeolites

A. Ghysels, S.L. Moors, K. Hemelsoet, K. De Wispelaere, M. Waroquier, G. Sastre, V. Van Speybroeck
Journal of Physical Chemistry C
119, 41, 23721-23734
2015
A1

Abstract 

The diffusion of olefins through 8-ring solid acid microporous zeolites is investigated using molecular dynamics simulations techniques and using a newly developed flexible force field. Within the context of the Methanol to Olefin (MTO) process and the observed product distribution, knowledge on the diffusion paths is essential to obtain molecular level control over the process conditions. Eight-ring zeotype materials are favorably used for the MTO process as they give a selective product distribution towards low carbon olefins. To investigate how composition, acidity and flexibility influence the diffusion paths of ethene and propene, a series of isostructural aluminosilicates (zeolites) and silicoaluminophosphates (AlPOs and SAPOs) are investigated with and without randomly distributed acidic sites. Distinct variations in diffusion of ethene are observed in terms of temperature, composition, acidity, and topology (AEI, CHA, AFX). In general, diffusion of ethene is an activated process for which free energy barriers for individual rings may be determined. We observe ring dependent diffusion behavior which can not solely be described in terms of the composition and topology of the rings. A new descriptor had to be introduced namely the accessible window area (AWA), inspired by implicit solvation models of proteins and small molecules. The AWA may be determined throughout the molecular dynamics trajectories and correlates well with the number of ring crossings at the molecular level and the free energy barriers for ring crossings from one cage to the other. The overall observed diffusivity is determined by molecular characteristics of individual rings for which AWA is a proper descriptor. Temperature-induced changes in framework dynamics and diffusivity may be captured by following the new descriptor throughout the simulations.

Normal mode analysis of macromolecular systems with the mobile block Hessian method

A. Ghysels, V. Van Speybroeck, D. Van Neck, B.R. Brooks, M. Waroquier
AIP Conference Proceedings
1642 (2015), 559
2015
P1

Abstract 

Until recently, normal mode analysis (NMA) was limited to small proteins, not only because the required energy minimization is a computationally exhausting task, but also because NMA requires the expensive diagonalization of a 3N(a) x 3N(a) matrix with N-a the number of atoms. A series of simplified models has been proposed, in particular the Rotation-Translation Blocks (RTB) method by Tama et al. for the simulation of proteins. It makes use of the concept that a peptide chain or protein can be seen as a subsequent set of rigid components, i.e. the peptide units. A peptide chain is thus divided into rigid blocks with six degrees of freedom each.

Recently we developed the Mobile Block Hessian (MBH) method, which in a sense has similar features as the RTB method. The main difference is that MBH was developed to deal with partially optimized systems. The position/orientation of each block is optimized while the internal geometry is kept fixed at a plausible - but not necessarily optimized - geometry. This reduces the computational cost of the energy minimization. Applying the standard NMA on a partially optimized structure however results in spurious imaginary frequencies and unwanted coordinate dependence. The MBH avoids these unphysical effects by taking into account energy gradient corrections. Moreover the number of variables is reduced, which facilitates the diagonalization of the Hessian.

In the original implementation of MBH, atoms could only be part of one rigid block. The MBH is now extended to the case where atoms can be part of two or more blocks. Two basic linkages can be realized: (1) blocks connected by one link atom, or (2) by two link atoms, where the latter is referred to as the hinge type connection. In this work we present the MBH concept and illustrate its performance with the crambin protein as an example.

Insight into the Effect of Water on the Methanol-to-Olefins Conversion in H-SAPO-34 from Molecular Simulations and in Situ Microspectroscopy

K. De Wispelaere, C.S. Wondergem, B. Ensing, K. Hemelsoet, E.J. Meijer, B.M. Weckhuysen, V. Van Speybroeck, J. Ruiz-Martinez
ACS Catalysis
6, 1991-2002
2016
A1

Abstract 

The role of water in the methanol-to-olefins (MTO) process over H-SAPO-34 has been elucidated by a combined theoretical and experimental approach, encompassing advanced molecular dynamics simulations and in-situ micro-spectroscopy. First principle calculations at the molecular level point out that water competes with methanol and propene for direct access to the Brønsted acid sites. This results in less efficient activation of these molecules, which are crucial for the formation of the hydrocarbon pool. Furthermore, lower intrinsic methanol reactivity towards methoxide formation has been observed. These observations are in line with a longer induction period observed from in-situ UV-Vis micro-spectroscopy experiments. These experiments revealed a slower and more homogeneous discoloration of H-SAPO-34, while in-situ confocal fluorescence microscopy confirmed the more homogeneous distribution and larger amount of MTO intermediates when co-feeding water. As such it is show that water induces a more efficient use of the H-SAPO-34 catalyst crystals at the microscopic level. The combined experimental theoretical approach gives a profound insight into the role of water on the catalytic process at the molecular and single particle level.

The enantioselectivity of the manganese-salen complex in the epoxidation of unfunctionalized olefins and the influence of grafting

T. Bogaerts, S. Wouters, P. Van der Voort, V. Van Speybroeck
Journal of Molecular Catalysis A: Chemical
Vol. 406, 106-113
2015
A1

Abstract 

Jacobsen’s complexes are famous for their usability for enantioselective epoxidations. However, the applicability of this catalytic system has been severely limited by several practical problems such as deactivation and separation after reaction. Grafting of Jacobsen-type complexes on solid supports is an attractive way to overcome these problems but led to a decrease in selectivity. A combined theoretical and experimental approach is presented to unravel the factors governing enantioselectivity. The importance of different substituents was determined by analyzing the transition state for the oxygen transfer using the full system as a model. An analysis of the asymmetric complex has shown an inherent tendency for a decreased selectivity due to the lack of specific bulky groups. Experimentally an immobilized Jacobsen catalyst on a metal organic framework (MIL-101) was synthesized which confirms the computational tendencies but the decrease in selectivity is limited, indicating that the MIL-101(Cr) is a suitable carrier for this complex.

Open Access version available at UGent repository

DOI 

10.1016/j.molcata.2015.05.020

Mechanistic investigation on the oxygen transfer with the manganese-salen complex

T. Bogaerts, S. Wouters, P. Van der Voort, V. Van Speybroeck
ChemCatChem
7 (17), 2711–2719
2015
A1

Abstract 

The most well-known application of salen complexes is the use of a chiral ligand loaded with manganese to form the Jacobsen complex. This organometallic catalyst is used in the epoxidation of unfunctionalized olefins and can achieve very high selectivities. Although this application was proposed many years ago, the mechanism of oxygen transfer remains a question until now. In this paper, the epoxidation mechanism is investigated by an ab initio kinetic modeling study. First of all a proper DFT functional is selected which yields the correct ordering of the various spin states. Our results show that the epoxidation proceeds via a radical intermediate. Starting from the radical intermediate, these results can explain the experiments with radical probes. The subtle influences in the transition state using the full Jacobsen catalyst explain the experimentally observed product distribution.

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