V. Van Speybroeck

Use of 3-Hydroxy-4-(trifluoromethyl)azetidin-2-ones as Building Blocks for the Preparation of Trifluoromethyl-Containing Aminopropanes, 1,3-Oxazinan-2-ones, Aziridines, and 1,4-Dioxan-2-ones

H.D. Thi, G. Le Nhat Thuy, S. Catak, V. Van Speybroeck, T. Van Nguyen, M. D'Hooghe
Synthesis-Stuttgart
50, 1439-1456
2018
A1

Abstract 

3-Hydroxy- 4-(trifluoromethyl)azetidin- 2-ones were efficiently synthesized from the corresponding 3-benzyloxy-β-lactams and successfully transformed into 3-chloro- 4-(trifluoromethyl)azetidin-2- one building blocks. The latter chlorides were shown to be eligible precursors for the construction of novel CF 3 -containing aminopropanes, 1,3-oxazinanes, 1,3-oxazinan-2- ones and aziridines. In addition, 3-hydroxy- 4-(trifluoromethyl)azetidin- 2-ones proved to be interesting substrates for the synthesis of novel 3-[2,2,2- trifluoro-1-(arylamino)ethyl]-1,4- dioxan-2- ones via intramolecular cyclization of 3-(2- hydroxyethoxy)-β-lactam intermediates.

DOI 

http://dx.doi.org/10.1055/s-0036-1591537

Understanding Brønsted-Acid Catalyzed Monomolecular Reactions of Alkanes in Zeolite Pores by Combining Insights from Experiment and Theory

J. Van der Mynsbrugge, A. Janda, L.-C. Lin, V. Van Speybroeck, M. Head-Gordon, A.T. Bell
ChemPhysChem
19 (4), 341-358
2018
A1

Abstract 

Acidic zeolites are effective catalysts for the cracking of large hydrocarbon molecules into lower molecular weight products required for transportation fuels. However, the ways in which the zeolite structure affects the catalytic activity at Brønsted protons are not fully understood. One way to characterize the influence of the zeolite structure on the catalysis is to study alkane cracking and dehydrogenation at very low conversion, conditions for which the kinetics are well defined. To understand the effects of zeolite structure on the measured rate coefficient (kapp), it is necessary to identify the equilibrium constant for adsorption into the reactant state (Kads-H+) and the intrinsic rate coefficient of the reaction (kint) at reaction temperatures, since kapp is proportional to the products of Kads-H+ and kint. We show that Kads-H+ cannot be calculated from experimental adsorption data collected near ambient temperature, but can, however, be estimated accurately from configurational-bias Monte Carlo (CBMC) simulations. Using monomolecular cracking and dehydrogenation of C3-C6 alkanes as an example, we review recent efforts aimed at elucidating the influence of the acid site location and the zeolite framework structure on the observed values of kapp and its components, Kads-H+ and kint.

DOI 

http://dx.doi.org/10.1002/cphc.201701084

Theoretical Insight into the Regioselective Ring-Expansions of Bicyclic Aziridinium Ions

E. Birsen Boydas, G. Tanriver, M. D'Hooghe, H-J. Ha, V. Van Speybroeck, S. Catak
Organic & Biomolecular Chemistry
16 (5), 796-806
2018
A1

Abstract 

Transient bicyclic aziridinium ions are known to undergo ring-expansion reactions, paving the way to functionalized nitrogen-containing heterocycles. In this study, the regioselectivity observed in the ring-expansion reactions of 1-azoniabicyclo[n.1.0]alkanes was investigated from a computational viewpoint to study the ring-expansion pathways of two bicyclic systems with different ring sizes. Moreover, several nucleophiles leading to different experimental results were investigated. The effect of solvation was taken into account using both explicit and implicit solvent models. This theoretical rationalization provides valuable insight into the observed regioselectivity and may be used as a predictive tool in future studies.

DOI 

http://dx.doi.org/10.1039/C7OB02253K

On the intrinsic dynamic nature of the rigid UiO-66 metal-organic framework

J. Hajek, C. Caratelli, R. Demuynck, K. De Wispelaere, L. Vanduyfhuys, M. Waroquier, V. Van Speybroeck
Chemical Science
9 (10), 2723-2732
2018
A1

Abstract 

UiO-66 is a showcase example of an extremely stable metal–organic framework, which maintains its structural integrity during activation processes such as linker exchange and dehydration. The framework can even accommodate a substantial number of defects without compromising its stability. These observations point to an intrinsic dynamic flexibility of the framework, related to changes in the coordination number of the zirconium atoms. Herein we follow the dynamics of the framework in situ, by means of enhanced sampling molecular dynamics simulations such as umbrella sampling, during an activation process, where the coordination number of the bridging hydroxyl groups capped in the inorganic Zr6(μ3-O)4(μ3-OH)4 brick is reduced from three to one. Such a reduction in the coordination number occurs during the dehydration process and in other processes where defects are formed. We observe a remarkable fast response of the system upon structural changes of the hydroxyl group. Internal deformation modes are detected, which point to linker decoordination and recoordination. Detached linkers may be stabilized by hydrogen bonds with hydroxyl groups of the inorganic brick, which gives evidence for an intrinsic dynamic acidity even in the absence of protic guest molecules. Our observations yield a major step forward in the understanding on the molecular level of activation processes realized experimentally but that is hard to track on a purely experimental basis.

Open Access version available at UGent repository
Green Open Access

DOI 

http://dx.doi.org/10.1039/C7SC04947A

How chain length and branching influence the alkene cracking reactivity on H-ZSM-5

P. Cnudde, K. De Wispelaere, L. Vanduyfhuys, R. Demuynck, J. Van der Mynsbrugge, M. Waroquier, V. Van Speybroeck
ACS Catalysis
8, 9579 − 9595
2018
A1

Abstract 

Catalytic alkene cracking on H-ZSM-5 involves a complex reaction network with many possible reaction routes and often elusive intermediates. Herein, advanced molecular dynamics simulations at 773 K, a typical cracking temperature, are performed to clarify the nature of the intermediates and to elucidate dominant cracking pathways at operating conditions. A series of C4-C8 alkene intermediates are investigated to evaluate the influence of chain length and degree of branching on their stability. Our simulations reveal that linear, secondary carbenium ions are relatively unstable, although their lifetime increases with carbon number. Tertiary carbenium ions, on the other hand, are shown to be very stable, irrespective of the chain length. Highly branched carbenium ions, though, tend to rapidly rearrange into more stable cationic species, either via cracking or isomerization reactions. Dominant cracking pathways were determined by combining these insights on carbenium ion stability with intrinsic free energy barriers for various octene β-scission reactions, determined via umbrella sampling simulations at operating temperature (773 K). Cracking modes A (3° → 3°) and B2 (3° → 2°) are expected to be dominant at operating conditions, whereas modes B1 (2° → 3°), C (2° → 2°), D2 (2° → 1°) and E2 (3° → 1°) are expected to be less important. All β-scission modes in which a transition state with primary carbocation character is involved have high intrinsic free energy barriers. Reactions starting from secondary carbenium ions will contribute less as these intermediates are short living at the high cracking temperature. Our results show the importance of simulations at operating conditions to properly evaluate the carbenium ion stability for β-scission reactions and to assess the mobility of all species in the pores of the zeolite.

Open Access version available at UGent repository
Gold Open Access

DOI 

http://dx.doi.org/10.1021/acscatal.8b01779

Extension of the QuickFF force field protocol for an improved accuracy of structural, vibrational, mechanical and thermal properties of Metal Organic Frameworks

L. Vanduyfhuys, S. Vandenbrande, J. Wieme, M. Waroquier, T. Verstraelen, V. Van Speybroeck
Journal of Computational Chemistry
39 (16), p. 999-1011
2018
A1

Abstract 

QuickFF was originally launched in 2015 to derive accurate force fields for isolated and complex molecular systems in a quick and easy way. Apart from the general applicability, the functionality was especially tested for metal-organic frameworks (MOFs), a class of hybrid materials consisting of organic and inorganic building blocks. Herein, we launch a new release of the QuickFF protocol which includes new major features to predict structural, vibrational, mechanical and thermal properties with greater accuracy, without compromising its robustness and transparant workflow. First, the ab initio data necessary for the fitting procedure may now also be derived from periodic models for the molecular system, as opposed to the earlier cluster-based models. This is essential for an accurate description of MOFs with one dimensional metal-oxide chains. Second, cross terms that couple internal coordinates (ICs) and anharmonic contributions for bond and bend terms are implemented. These features are essential for a proper description of vibrational and thermal properties. Third, the fitting scheme was modified to improve robustness and accuracy. The new features are tested on MIL-53(Al), MOF-5, CAU-13 and NOTT-300. As expected, periodic input data is proven to be essential for a correct description of structural, vibrational and thermodynamic properties of MIL-53(Al). Bulk moduli and thermal expansion coefficients of MOF-5 are very accurately reproduced by static and dynamic simulations using the newly derived force fields which include cross terms and anharmonic corrections. For the flexible materials CAU-13 and NOTT-300, the transition pressure is accurately
predicted provided cross terms are taken into account.

Open Access version available at UGent repository
Gold Open Access

DOI 

http://dx.doi.org/10.1002/jcc.25173

Formation of Fluorinated Amido Esters through Unexpected C3-C4 Bond Fission in 4-Trifluoromethyl-3-oxo-β-lactams

H.D. Thi, H. Goossens, D. Hertsen, V. Otte, T. Van Nguyen, V. Van Speybroeck, M. D'Hooghe
Chemistry - An Asian Journal
13 (4), 421-431
2018
A1

Abstract 

4-Trifluoromethyl-3-oxo-β-lactams were unexpectedly transformed into 2-[(2,2-difluorovinyl)amino]-2-oxoacetates as major products, accompanied by minor amounts of 2-oxo-2-[(2,2,2-trifluoroethyl)amino]acetates, upon treatment with alkyl halides and triethylamine in DMSO. This peculiar C3-C4 bond fission reactivity was investigated in-depth, from both an experimental and a computational point of view, in order to shed light on the underlying reaction mechanism.

DOI 

http://dx.doi.org/10.1002/asia.201701636

Thermodynamic insight into stimuli-responsive behavior of soft porous crystals

L. Vanduyfhuys, S.M.J. Rogge, J. Wieme, S. Vandenbrande, G. Maurin, M. Waroquier, V. Van Speybroeck
Nature Communications
9, 1, 204
2018
A1

Abstract 

Knowledge of the thermodynamic potential in terms of the independent variables allows to characterize the macroscopic state of the system. However, in practice, it is difficult to access this potential experimentally due to irreversible transitions that occur between equilibrium states. A showcase example of sudden transitions between (meta)stable equilibrium states is observed for soft porous crystals possessing a network with long-range structural order, which can transform between various states upon external stimuli such as pressure, temperature and guest adsorption. Such phase transformations are typically characterized by large volume changes and may be followed experimentally by monitoring the volume change in terms of certain external triggers. Herein, we present a generalized thermodynamic approach to construct the underlying Helmholtz free energy as a function of the state variables that governs the observed behaviour based on microscopic simulations. This concept allows a unique identification of the conditions under which a material becomes flexible.

Open Access version available at UGent repository
Gold Open Access

DOI 

http://dx.doi.org/10.1038/s41467-017-02666-y

The Importance of Cell Shape Sampling To Accurately Predict Flexibility in Metal-Organic Frameworks

S.M.J. Rogge, S. Caroes, R. Demuynck, M. Waroquier, V. Van Speybroeck, A. Ghysels
Journal of Chemical Theory and Computation
14 (3), 1186-1197
2018
A1

Abstract 

In this work, the influence of cell shape sampling on the predicted stability of the different metastable phases in flexible metal–organic frameworks at finite temperatures is investigated. The influence on the free energy by neglecting cell shape sampling is quantified for the prototypical MIL-53(Al) and the topical DUT-49(Cu). This goal is achieved by constructing free energy profiles in ensembles either in which the phase space associated with the cell shape is sampled explicitly or in which the cell shape is kept fixed. When neglecting cell shape sampling, thermodynamic integration of the hydrostatic pressure yields unreliable free energy profiles that depend on the choice of the fixed cell shape. In this work, we extend the thermodynamic integration procedure via the introduction of a generalized pressure, derived from the Lagrangian strain tensor and the second Piola–Kirchhoff tensor. Using this generalized procedure, the dependence on the unit cell shape can be eliminated, and the inaccuracy in free energy stemming from the lack of cell shape sampling can be uniquely quantified. Finally, it is shown that the inaccuracy in free energy when fixing the cell shape at room temperature stems mainly from entropic contributions for both MIL-53(Al) and DUT-49(Cu).

DOI 

http://dx.doi.org/10.1021/acs.jctc.7b01134

Elucidating the Vibrational Fingerprint of the Flexible Metal-Organic Framework MIL-53(Al) Using a Combined Experimental/Computational Approach

A.E.J. Hoffman, L. Vanduyfhuys, I. Nevjestic, J. Wieme, S.M.J. Rogge, H. Depauw, P. Van der Voort, H. Vrielinck, V. Van Speybroeck
Journal of Physical Chemistry C
122, 5, 2734-2746
2018
A1

Abstract 

In this work mid-infrared (mid-IR), far-IR, and Raman spectra are presented for the distinct (meta)stable phases of the flexible metal-organic framework MIL-53(Al). Static density functional theory (DFT) simulations are performed allowing for the identification of all IR active modes, which is unprecedented in the low-frequency region. A unique vibrational fingerprint is revealed, resulting from aluminum-oxide backbone stretching modes, which can be used to clearly distinguish the IR spectra of the closed- and large-pore phases. Furthermore, molecular dynamics simulations based on a DFT description of the potential energy surface enable to determine the theoretical Raman spectrum of the closed- and large-pore phases for the first time. An excellent correspondence between theory and experiment is observed. Both the low-frequency IR and Raman spectra show major differences in vibrational modes between the closed- and large-pore phases indicating changes in lattice dynamics between the two structures. In addition, several collective modes related to the breathing mechanism in MIL-53(Al) are identified. In particular, we rationalize the importance of the trampoline-like motion of the linker for the phase transition.

Open Access version available at UGent repository
Gold Open Access

DOI 

http://dx.doi.org/10.1021/acs.jpcc.7b11031

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