M. Waroquier

Solved? The reductive radiation chemistry of alanine

E. Pauwels, H. De Cooman, M. Waroquier, E. Hole, E. Sagstuen
Physial Chemistry Chemical Physics
16(6), 2475-2482
2014
A1

Abstract 

The structural changes throughout the entire reductive radiation-induced pathway of l-α-alanine are solved on an atomistic level with the aid of periodic DFT and nudged elastic band (NEB) simulations. This yields unprecedented information on the conformational changes taking place, including the protonation state of the carboxyl group in the "unstable" and "stable" alanine radicals and the internal transformation converting these two radical variants at temperatures above 220 K. The structures of all stable radicals were verified by calculating EPR properties and comparing those with experimental data. The variation of the energy throughout the full radiochemical process provides crucial insight into the reason why these structural changes and rearrangements occur. Starting from electron capture, the excess electron quickly localizes on the carbon of a carboxyl group, which pyramidalizes and receives a proton from the amino group of a neighboring alanine molecule, forming a first stable radical species (up to 150 K). In the temperature interval 150-220 K, this radical deaminates and deprotonates at the carboxyl group, the detached amino group undergoes inversion and its methyl group sustains an internal rotation. This yields the so-called "unstable alanine radical". Above 220 K, triggered by the attachment of an additional proton on the detached amino group, the radical then undergoes an internal rotation in the reverse direction, giving rise to the "stable alanine radical", which is the final stage in the reductive radiation-induced decay of alanine.

Open Access version available at UGent repository

Vanadium Metal-Organic Frameworks: Structures and Applications

P. Van der Voort, K. Leus, Y-Y Liu, M. Vandichel, V. Van Speybroeck, M. Waroquier, S. Biswas
New Journal of Chemistry
38, 1853-1867
2014
A1

Abstract 

This perspective review paper describes the V-containing Metal-Organic Framworks that have been developed since the first systematic reports on MOFs almost 15 years ago. These hybrid crystalline materials, containing V(III) or V(IV) as metal nodes show interesting behaviour in oxidation catalysis and gas sorption. A significant amount of papers has appeared on the use of these structures in gas (hydrocarbon, CO2) separation. Promising future research and development of V-MOFs is suggested.

Open Access version available at UGent repository

Molecular dynamics kinetic study on the zeolite-catalyzed benzene methylation in ZSM-5

S.L. Moors, K. De Wispelaere, J. Van der Mynsbrugge, M. Waroquier, V. Van Speybroeck
ACS Catalysis
2013 (3), 2556–2567
2013
A1

Abstract 

The methylation of arenes is a key step in the production of hydrocarbons from methanol over acidic zeolites. We performed ab initio static and molecular dynamics free energy simulations of the benzene methylation in H-ZSM-5 to determine the factors that influence the reaction kinetics. Special emphasis is given to the effect of surrounding methanol molecules on the methylation kinetics. It is found that for higher methanol loadings methylation may also occur from a protonated methanol cluster, indicating that the exact location of the Brønsted acid site is not essential for the zeolite-catalyzed methylation reaction. However, methylations from a protonated methanol cluster exhibit higher free energy barriers than a methylation from a single methanol molecule. Finally, comparison with a pure methanol solvent reaction environment indicates that the main role of the zeolite during the methylation of benzene is to provide the acidic proton and to create a polar environment for the reaction. The metadynamics approach, which is specifically designed to sample rare events, allows exploring new reaction pathways, which take into account the flexibility of the framework and additional guest molecules in the pores and channels of the zeolite framework. This approach goes beyond the often applied static calculations to determine reaction kinetics.

Crystal structure prediction for supersaturated AZO : the case of Zn3Al2O6

K. Rijpstra, S. Cottenier, M. Waroquier, V. Van Speybroeck
CrystEngComm
2013 (15), 10440-10444
2013
A1

Abstract 

Increasing the Al concentration in Al-doped ZnO (AZO) is one way of improving the conductivity of this transparent conductive oxide (TCO). Beyond a certain concentration, an unwanted secondary phase develops with a low conductivity. Its stoichiometry is Zn3Al2O6, and its crystal structure has not yet been convincingly determined. By applying unbiased ab initio structure prediction tools, we predict the crystal structure of Zn3Al2O6 to be monoclinic with space group Pm. It can be described as a nanofabric, with one-dimensional Al2O3 wires penetrating a ZnO matrix. This crystal has a formation energy that is lower than any structure proposed before, and is consistent with all available experimental information. Knowledge of the nature of this phase can help to avoid its formation and therefore to engineer AZO crystals with an increased level of Al-doping and associated increased conductivity.

New Functionalized Metal–Organic Frameworks MIL-47-X (X = −Cl, −Br, −CH3, −CF3, −OH, −OCH3): Synthesis, Characterization, and CO2 Adsorption Properties

S. Biswas, D.E.P. Vanpoucke, T. Verstraelen, M. Vandichel, S. Couck, K. Leus, Y-Y Liu, M. Waroquier, V. Van Speybroeck, J.F.M. Denayer, P. Van der Voort
Journal of Physical Chemistry C
117 (44), 22784–22796
2013
A1

Abstract 

Six new functionalized vanadium hydroxo terephthalates [VIII(OH)(BDC-X)]•n(guests) (MIL-47(VIII)-X-AS) (BDC = 1,4-benzenedicarboxylate; X = -Cl; -Br, -CH3, -CF3, -OH, -OCH3; AS = as-synthesized) along with the parent MIL-47 were synthesized under rapid microwave-assisted hydrothermal conditions (170 ºC, 30 min, 150 W). The unreacted H2BDC-X and/or occluded solvent molecules can be removed by thermal activation under vacuum leading to the empty-pore forms of the title compounds (MIL-47(VIV)-X). Except pristine MIL-47 (+III oxidation state), the vanadium atoms in all the evacuated functionalized solids stayed in +IV oxidation state. The phase purity of the compounds was ascertained by X-ray powder diffraction (XRPD), diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy, Raman, thermogravimetric (TG), and elemental analysis. The structural similarity of the filled and empty-pore forms of the functionalized compounds with the respective forms of parent MIL-47 was verified by cell parameter determination from XRPD data. TGA and temperature-dependent XRPD (TDXRPD) experiments in air atmosphere indicate high thermal stability in the range 330-385 ºC. All the thermally activated compounds exhibit significant microporosity (SLangmuir in the range 418-1104 m2 g-1), as verified by the N2 and CO2 sorption analysis. Among the six functionalized compounds, MIL-47(VIV)-OCH3 shows the highest CO2 uptake, demonstrating the determining role of functional groups on the CO2 sorption behaviour. For this compound and pristine MIL-47(VIV), Widom particle insertion simulations were performed based on ab initio calculated crystal structures. The theoretical Henry coefficients show a good agreement with the experimental values, and calculated isosurfaces for the local excess chemical potential indicate the enhanced CO2 affinity is due to two effects: (i) the interaction between the methoxy group and CO2 and (ii) the collapse of the MIL-47(VIV)-OCH3 framework.

Identification of intermediates in zeolite-catalyzed reactions using in-situ UV/Vis micro-spectroscopy and a complementary set of molecular simulations

K. Hemelsoet, Q. Qian, T. De Meyer, K. De Wispelaere, B. De Sterck, B.M. Weckhuysen, M. Waroquier, V. Van Speybroeck
Chemistry - A European Journal
19, 49, 16595-16606
2013
A1

Abstract 

The optical absorption properties of (poly)aromatic hydrocarbons occluded in a nanoporous environment were investigated by theoretical and experimental methods. The carbonaceous species are an essential part of a working catalyst for the methanol-to-olefins (MTO) process. In situ UV/Vis microscopy measurements on methanol conversion over the acidic solid catalysts H-SAPO-34 and H-SSZ-13 revealed the growth of various broad absorption bands around 400, 480, and 580 nm. The cationic nature of the involved species was determined by interaction of ammonia with the methanol-treated samples. To determine which organic species contribute to the various bands, a systematic series of aromatics was analyzed by means of time-dependent density functional theory (TDDFT) calculations. Static gas-phase simulations revealed the influence of structurally different hydrocarbons on the absorption spectra, whereas the influence of the zeolitic framework was examined by using supramolecular models within a quantum mechanics/molecular mechanics framework. To fully understand the origin of the main absorption peaks, a molecular dynamics (MD) study on the organic species trapped in the inorganic host was essential. During such simulation the flexibility is fully taken into account and the effect on the UV/Vis spectra is determined by performing TDDFT calculations on various snapshots of the MD run. This procedure allows an energy absorption scale to be provided and the various absorption bands determined from in situ UV/Vis spectra to be assigned to structurally different species.

Synthesis modulation as a tool to increase the catalytic activity of MOFs: the unique case of UiO-66(Zr)

F. Vermoortele, B. Bueken, G. Le Bars, B. Van de Voorde, M. Vandichel, K. Houthoofd, A. Vimont, M. Daturi, M. Waroquier, V. Van Speybroeck, C. Kirschhock, D. De Vos
JACS (Journal of the American Chemical Society)
135 (31), 11465–11468
2013
A1

Abstract 

The catalytic activity of the zirconium terephthalate UiO-66(Zr) can be drastically increased by using a modulation approach. The combined use of trifluoroacetic acid and HCl during the synthesis results in a highly crystalline material, with partial substitution of terephthalates by trifluoroacetate. Thermal activation of the material leads not only to dehydroxylation of the hexanuclear Zr cluster but also to post-synthetic removal of the trifluoroacetate groups, resulting in a more open framework with a large number of open sites. Consequently, the material is a highly active catalyst for several Lewis acid catalyzed reactions.

Trans Effect and Trans Influence: Repulsion, rather than Competition for Donation

B. Pinter, V. Van Speybroeck, M. Waroquier, P. Geerlings, F. De Proft
Physical Chemistry Chemical Physics (PCCP)
15 (40), 17354-17365
2013
A1

Abstract 

The trans effect and trans influence were investigated and rationalized in the aminolysis, a typical nucleophilic substitution reaction, of trans-TPtCl2NH3 complexes (T = NH3, PH3, CO and C2H4) using energy decomposition analysis, both along the reaction paths and on the stationary points, and Natural Orbital for Chemical Valence analysis. In order to scrutinize the underlying principles and the origin of the kinetic trans effect, plausible structural constraints were introduced in the decomposition analysis, which allowed eliminating the distance dependence of the interaction energy components. It was established that the trans effect can be rationalized with the interaction of the TPtCl2 and NH3 fragments in the reactant state and TPtCl2 and (NH3)2 fragments in the transition state. It was evinced quantitatively that the σ-donor ability of T indeed controls the stability of the reactant, whereas in the case of π-acids, backdonation stabilizes the transition state, for which conceptually two mechanisms are available: intrinsic and induced π-backdonation. In the destabilization of the reactant and also in the labilization of the leaving group (trans influence) repulsion plays a more important role than orbital sharing effects, which are the cornerstones of the widely accepted interpretations of the trans influence, such as competition for donation or limitation of the donation of the leaving group by the trans ligand T. This repulsive interaction was rationalized both in terms of donated electron density and also in the molecular orbital framework. NOCV orbitals indeed clearly show that the σ-trans effect can be envisioned as a donation from the trans ligand not only to the metal but also to the σ* orbital of the metal-leaving group bond, which manifests as a repulsion between the metal and the leaving group.

Enthalpy and entropy barriers explain the effects of topology on the kinetics of zeolite-catalyzed reactions

J. Van der Mynsbrugge, J. De Ridder, K. Hemelsoet, M. Waroquier, V. Van Speybroeck
Chemistry - A European Journal
19 (35), 11568-11576
2013
A1

Abstract 

The methylation of ethene, propene, and trans-2-butene on zeolites H-ZSM-58 (DDR), H-ZSM-22 (TON), and H-ZSM-5 (MFI) is studied to elucidate the particular influence of topology on the kinetics of zeolite-catalyzed reactions. H-ZSM-58 and H-ZSM-22 are found to display overall lower methylation rates compared to H-ZSM-5 and also different trends in methylation rates with increasing alkene size. These variations may be rationalized based on a decomposition of the free-energy barriers into enthalpic and entropic contributions, which reveals that the lower methylation rates on H-ZSM-58 and H-ZSM-22 have virtually opposite reasons. On H-ZSM-58, the lower methylation rates are caused by higher enthalpy barriers, owing to inefficient stabilization of the reaction intermediates in the large cage-like pores. On the other hand, on H-ZSM-22, the methylation rates mostly suffer from higher entropy barriers, because excessive entropy losses are incurred inside the narrow-channel structure. These results show that the kinetics of crucial elementary steps hinge on the balance between proper stabilization of the reaction intermediates inside the zeolite pores and the resulting entropy losses. These fundamental insights into their inner workings are indispensable for ultimately selecting or designing better zeolite catalysts.

Insight in the activity and diastereoselectivity of various Lewis acid catalysts for the citronellal cyclization

M. Vandichel, F. Vermoortele, S. Cottenie, D. De Vos, M. Waroquier, V. Van Speybroeck
Journal of Catalysis
305, 118-129
2013
A1

Abstract 

Industrial (-)-menthol production generally relies on the hydrogenation of (-)-isopulegol, which is in turn produced with high selectivity by cyclization of (+)-citronellal. This paper uses a combined theoretical and experimental approach to study the activity and selectivity of three Lewis acid catalysts for this reaction, namely ZnBr2, aluminum tris(2,6-diphenylphenoxide) (ATPH) and the heterogeneous metal-organic framework Cu3BTC2 (BTC = benzene-1,3,5-tricarboxylate). ATPH is a strong Lewis acid homogeneous catalyst with bulky ligands which provides very high selectivities for the desired stereo-isomer (> 99 %). The performance of the catalysts was evaluated as a function of temperature, which revealed that higher catalyst activity allows working at lower temperatures and improves the selectivity for isopulegol. The selectivity distribution is kinetically driven for ZnBr2 and ATPH. The theoretical selectivity distributions rely on the determination of an extensive set of diastereomeric transition states, for which the differences in free energy have been calculated using a complementary set of ab initio techniques. Given the sensitivity of the selectivity to small Gibbs free energy differences, the agreement between experimental and theoretical selectivities is satisfactory. On basis of the obtained insights rational design of new catalysts may be obtained. As proof of concept, the hypothetical Cu3(BTC-(NO2)3)2 Lewis catalyst – in which each phenyl hydrogen of the BTC ligand is replaced by a nitro group - is predicted to be very selective.

Open Access version available at UGent repository

Pages

Subscribe to RSS - M. Waroquier