M. Waroquier

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

PPV Polymerization via the Gilch Route: Diradical Character of Monomers

J.D. Nikolic, S. Wouters, J. Romanova, A. Shimizu, B. Champagne, T. Junkers, D. Vanderzande, D. Van Neck, M. Waroquier, V. Van Speybroeck, S. Catak
Chemistry - A European Journal
21, 19176-19185
2015
A1

Abstract 

Despite various studies on the polymerization of poly(p-phenylene vinylene) (PPV) through different precursor routes, detailed mechanistic knowledge on the individual reaction steps and intermediates is still incomplete. The present study aims to gain more insight into the radical polymerization of PPV through the Gilch route. The initial steps of the polymerization involve the formation of a p-quinodimethane intermediate, which spontaneously self-initiates through a dimerization process leading to the formation of diradical species; chain propagation ensues on both sides of the diradical or chain termination occurs by the formation of side products, such as [2.2]paracyclophanes. Furthermore, different p-quinodimethane systems were assessed with respect to the size of their aromatic core as well as the presence of heteroatoms in/on the conjugated system. The nature of the aromatic core and the specific substituents alter the electronic structure of the p-quinodimethane monomers, affecting the mechanism of polymerization. The diradical character of the monomers has been investigated with several advanced methodologies, such as spin-projected UHF, CASSCF, CASPT2, and DMRG calculations. It was shown that larger aromatic cores led to a higher diradical character in the monomers, which in turn is proposed to cause rapid initiation.

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

Advances in theory and their application within the field of zeolite chemistry

V. Van Speybroeck, K. Hemelsoet, L. Joos, M. Waroquier, R.G. Bell, C.R.A. Catlow
Chemical Society Reviews
Vol. 44 , 7044-7111
2015
A1

Abstract 

Zeolites are versatile and fascinating materials which are vital for a wide range of industries, due to their unique structural and chemical properties, which are the basis of applications in gas separation, ion exchange and catalysis. Given their economic impact, there is a powerful incentive for smart design of new materials with enhanced functionalities to obtain the best material for a given application. Over the last decades, theoretical modeling has matured to a level that model guided design has become within reach. Major hurdles have been overcome to reach this point and almost all contemporary methods in computational materials chemistry are actively used in the field of modeling zeolite chemistry and applications. Integration of complementary modeling approaches is necessary to obtain reliable predictions and rationalizations from theory. A close synergy between experimentalists and theoreticians has led to a deep understanding of the complexity of the system at hand, but also allowed the identification of shortcomings in current theoretical approaches. Inspired by the importance of zeolite characterization which can now be performed at the single atom and single molecule level from experiment, computational spectroscopy has grown in importance in the last decade. In this review most of the currently available modeling tools are introduced and illustrated on the most challenging problems in zeolite science. Directions for future model developments will be given.

Open Access version available at UGent repository

On the Possibility of [1,5] Sigmatropic Shifts in Bicyclo[4.2.0]octa-2,4-dienes

H. Goossens, J.M. Winne, S. Wouters, L. Hermosilla, P. J. De Clercq, M. Waroquier, V. Van Speybroeck, S. Catak
Journal of Organic Chemistry
80 (5) 2609-2620
2015
A1

Abstract 

The thermal equilibration of the methyl esters of endiandric acids D and E was subject to a computational study. An electrocyclic pathway via an electrocyclic ring opening followed by a ring flip and a subsequent electrocyclization proposed by Nicolaou [Chem. Soc. Rev. 2009], was computationally explored. The free energy barrier for this electrocyclic route was shown to be very close to the bicyclo[4.2.0]octa-2,4-diene reported by Huisgen [Tet. Lett. 1968]. Furthermore, the possibility of a [1,5] sigmatropic alkyl group shift of bicyclo[4.2.0]octa-2,4-diene systems at high temperatures was explored in a combined computational and experimental study. Calculated reaction barriers for a biradical-mediated stepwise [1,5] sigmatropic alkyl group shift were shown to be comparable with the reaction barriers for the bicyclo[4.1.0]hepta-2,4-diene (norcaradiene) walk rearrangement, whereas calculated reaction barriers for a concerted [1,5] sigmatropic alkyl group shift were found to be higher in energy. However, the stepwise pathway is suggested to only be feasible for appropriately substituted compounds. Experiments conducted on a deuterated analogous diol derivative confirmed the calculated (large) differences in barriers between electrocyclic and sigmatropic pathways.

Elucidating the Structural Isomerism of Fluorescent Strigolactone Analogue CISA-1

H. Goossens, T.S.A Heugebaert, B. Dereli, M. Van Overtveldt, O. Karahan, I. Doğan, M. Waroquier, V. Van Speybroeck, V. Aviyente, S. Catak, C.V. Stevens
European Journal of Organic Chemistry
2015 (6), 1211–1217
2015
A1

Abstract 

The synthesis of a new potent strigolactone analogue (CISA-1), resulting in the formation of two interconverting structural isomers, which could not be identified, was recently reported by Rasmussen et al [Molecular Plant, 2013, 6, 100]. In the present study, a combined computational and experimental approach is used to identify the exact nature of these structural isomers. While standard experimental techniques were not able to determine the identity of the isomers, chromatographic methods excluded E/Z isomerisation. Computational 1H NMR chemical shift values and DFT calculations on interconversion barriers strongly suggest that the CISA-1 isomers were interconverting (Z)-configured atropisomers.

Au@UiO-66: a base free oxidation catalyst

K. Leus, P. Concepcion, M. Vandichel, M. Meledina, A. Grirrane, D. Esquivel, S. Turner, D. Poelman, M. Waroquier, V. Van Speybroeck, G. Van Tendeloo, H. Garcia, P. Van der Voort
RSC Advances
5 (29), 22334–22342
2015
A1

Abstract 

We present the in situ synthesis of Au nanoparticles within the Zr based Metal Organic Framework, UiO-66. The resulting Au@UiO-66 materials were characterized by means of N2 sorption, XRPD, UV-Vis, XRF, XPS and TEM analysis. The Au nanoparticles (NP) are homogeneously distributed along the UiO-66 host matrix when using NaBH4 or H2 as reducing agents. The Au@UiO-66 materials were evaluated as catalysts in the oxidation of benzyl alcohol and benzyl amine employing O2 as oxidant. The Au@MOF materials exhibit a very high selectivity towards the ketone (up to 100 %). Regenerability and stability tests demonstrate that the Au@UiO-66 catalyst can be recycled with a negligible loss of Au species and no loss of crystallinity. In situ IR measurements of UiO-66 and Au@UiO-66-NaBH4, before and after treatment with alcohol, showed an increase in IR bands that can be assigned to a combination of physisorbed and chemisorbed alcohol species. This was confirmed by velocity power spectra obtained from the molecular dynamics simulations. Active peroxo and oxo species on Au could be visualized with Raman analysis.

Open Access version available at UGent repository

Active site engineering in UiO-66 type metal-organic frameworks by intentional creation of defects: a theoretical rationalization

M. Vandichel, J. Hajek, F. Vermoortele, D. De Vos, M. Waroquier, V. Van Speybroeck
CrystEngComm
17 (2), 395-406
2015
A1

Abstract 

The catalytic activity of the Zr-benzenedicarboxylate (Zr-BDC) UiO-66 can be drastically increased in the absence of part of the linkers, as it removes the full coordination of the framework metal ions and leads to open sites. As a result, metal centers become more accessible and thus more active for Lewis acid catalysed reactions. Addition of modulators (MDL) to the synthesis mixture can create more linker deficiencies (Vermoortele et al., J Am Chem Soc, 2013, 135, 11465) and can lead to a significant increase of the catalytic activity due to the creation of a larger number of open sites. In this paper, we rationalize the function of the modulators under real synthesis conditions by the construction of free energy diagrams. The UiO-66 type materials form a very appropriate test case as the effect of addition of modulators hydrochloric acid (HCl) and trifluoroacetate (TFA) has been intensively investigated experimentally for the synthesis process and post-synthetic thermal activation. In synthesis conditions, direct removal of BDC linkers requires a high free energy but replacement of such linker by one or more TFA species might occur especially at high TFA:BDC ratios in the reaction mixture. The presence of HCl furthermore enhances the creation of defect structures. Post-synthesis activation procedures at higher temperatures lead to a substantial removal of the species coordinated to the Zr bricks creating open metal sites. A mechanistic pathway is presented for the dehydroxylation process of the hexanuclear Zr cluster. For the citronellal cyclization, we show that the presence of some residual TFA in the structure may lead to faster reactions in complete agreement with experiment. Hirshfeld-e partial charges for the Zr ions have been computed to investigate their sensitivity to substituent effects; a strong correlation with the experimental Hammett parameters, and with the rates of the citronellal cyclization is found. The theoretical rationalization may serve as a basis for detailed active site engineering studies.

Open Access version available at UGent repository

How zeolitic acid strength and composition alter the reactivity of alkenes and aromatics towards methanol

M.W. Erichsen, K. De Wispelaere, K. Hemelsoet, S.L. Moors, T. Deconinck, M. Waroquier, S. Svelle, V. Van Speybroeck, U. Olsbye
Journal of Catalysis
328, 186-196
2015
A1

Abstract 

This work encompasses a combined experimental and theoretical assessment of how zeolitic acid strength and composition affects acid-catalysed methylation reactions. Overall, higher methylation rates were observed over the material with higher acid strength. Co-reactions of methanol with benzene at 250 degrees C over the two isostructural AFI materials H-SSZ-24 and H-SAPO-5 revealed large differences in selectivity. While the stronger acidic H-SSZ-24 mainly produced toluene and polymethylbenzenes, high yields of C4+ aliphatics were observed over H-SAPO-5. These results strongly suggest that alkene methylation was preferred over H-SAPO-5 even at very low conversion during methanol/benzene co-reactions. Furthermore, a comparison of benzene and propene methylation at 350-400 degrees C revealed a significantly faster rate of benzene than propene methylation in H-SSZ-24, whereas the rates of benzene and propene methylation were similar in H-SAPO-5. The observed difference in reactivity of the two hydrocarbons in both catalysts could be understood by careful analysis of various molecular dynamics simulations of the co-adsorbed complexes. The probability to form protonated methanol was, as expected, higher in the more acidic material. However, in H-SSZ-24, the probability for methanol protonation was higher when co-adsorbed with benzene than when co-adsorbed with propene, while the same was not observed in H-SAPO-5. Furthermore, it was found that benzene and methanol are more likely to form a reactive co-adsorbed complex in H-SSZ-24 compared to propene and methanol, while the opposite was observed for H-SAPO-5. This work shows that molecular dynamics simulations provide insights into the adsorption behaviour of guest molecules in large pore AFI materials. The obtained insights correlate with the experimentally observed reactivities. (C) 2015 Elsevier Inc. All rights reserved.

Open Access version available at UGent repository

Active site engineering in UiO-66 type Metal Organic Frameworks by intentional creation of defects : A theoretical rationalization

M. Vandichel, J. Hajek, F. Vermoortele, M. Waroquier, D. De Vos, V. Van Speybroeck
CrystEngComm
First published online 15 Sep 2014
2014
A1
Published while none of the authors were employed at the CMM

Abstract 

The catalytic activity of the Zr-benzenedicarboxylate (Zr-BDC) UiO-66 can be drastically increased in the absence of part of the linkers, as it removes the full coordination of the framework metal ions and leads to open sites. As a result, metal centers become more accessible and thus more active for Lewis acid catalysed reactions. Addition of modulators (MDL) to the synthesis mixture can create more linker deficiencies (Vermoortele et al., J Am Chem Soc, 2013, 135, 11465) and can lead to a significant increase of the catalytic activity due to the creation of a larger number of open sites. In this paper, we rationalize the function of the modulators under real synthesis conditions by the construction of free energy diagrams. The UiO-66 type materials form a very appropriate test case as the effect of addition of modulators HCl and trifluoroacetate (TFA) has been intensively investigated experimentally for the synthesis process and post-synthetic thermal activation. In synthesis conditions, direct removal of BDC linkers requires a high free energy but replacement of such linker by one or more TFA species might occur especially at high TFA:BDC ratios in the reaction mixture. The presence of HCl furthermore enhances the creation of defect structures. Post-synthesis activation procedures at higher temperatures lead to a substantial removal of the species coordinated to the Zr bricks creating open metal sites. A mechanistic pathway is presented for the dehydroxylation process of the hexanuclear Zr cluster. For the citronellal cyclization, we show that the presence of some residual TFA in the structure may lead to faster reactions in complete agreement with experiment. Hirshfeld-e partial charges for the Zr ions have been computed to investigate their sensitivity to substituent effects; a strong correlation with the experimental Hammett parameters, and with the rates of the citronellal cyclization is found. The theoretical rationalization may serve as a basis for detailed active site engineering studies.

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