V. Van Speybroeck

On the convergence of atomic charges with the size of the enzymatic environment

D.E.P. Vanpoucke, J. Olah, F. De Proft, V. Van Speybroeck, G. Roos
Journal of Chemical Information and Modeling (JCIM)
Volume 55 Issue 3 page 564–571
2015
A1

Abstract 

Atomic charges are a key concept to give more insight into the electronic structure and chemical reactivity. The Hirshfeld-I partitioning scheme applied to the model protein human 2-cysteine peroxiredoxin thioredoxin peroxidase B is used to investigate how large a protein fragment needs to be in order to achieve convergence of the atomic charge of both, neutral and negatively charged residues. Convergence in atomic charges is rapidly reached for neutral residues, but not for negatively charged ones. This study pinpoints difficulties on the road towards accurate modeling of negatively charged residues of large biomolecular systems in a multiscale approach.

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

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
First published online 15 May 2015
2015
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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.

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
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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.

Accelerated living cationic ring-opening polymerization of a methyl ester functionalized 2-oxazoline monomer

P.J.M. Bouten, D. Hertsen, M. Vergaelen, B. Monnery, M.A. Boerman, H. Goossens, S. Catak, J.C.M. van Hest, V. Van Speybroeck, R. Hoogenboom
Polymer Chemistry
6, 514-518
2015
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Abstract 

Kinetic studies on the homo- and copolymerization of 2-methoxycarboxyethyl-2-oxazoline (MestOx) with 2-methyl-2-oxazoline (MeOx) and 2-ethyl-2-oxazoline (EtOx) were performed. For the homopolymerisation of MestOx an increased propagation rate constant was observed compared to MeOx and EtOx while the copolymerization of MestOx with MeOx or EtOx unexpectedly revealed slower incorporation of MestOx. Density functional theory (DFT) calculations show that nearby MestOx residues in the living chain can activate both the oxazolinium chain end and the attacking monomer, stabilizing the propagation transition state, leading to faster homopolymerisation of MestOx. These effects also accelerate incorporation of both monomers in the copolymerisations. However, since MeOx is shown to be more nucleophilic than MestOx, the incorporation order is reversed in the copolymerisations.

Open Access version available at UGent repository

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
2015 (5), 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

Complex reaction environments and competing reaction mechanisms in zeolite catalysis: insights from advanced molecular dynamics

K. De Wispelaere, B. Ensing, A. Ghysels, E.J. Meijer, V. Van Speybroeck
Chemistry - A European Journal
21 (26), 9385-9396
2015
A1

Abstract 

The methanol to olefins process is a show case example of complex zeolite-catalyzed chemistry. At real operating conditions, many factors such as framework flexibility, adsorption of various guest molecules and competitive reaction pathways, affect reactivity. In this paper we show the strength of first principle molecular dynamics techniques to capture this complexity by means of two case studies. Firstly, the adsorption behavior of methanol and water in H-SAPO-34 at 350 °C is investigated. Hereby we observed an important degree of framework flexibility and proton mobility. Secondly, we studied the methylation of benzene by methanol via a competitive direct and stepwise pathway in the AFI topology. Both case studies clearly show that a first principle molecular dynamics approach enables to obtain unprecedented insights into zeolite-catalyzed reactions at the nanometer scale.

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

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