V. Van Speybroeck

Towards metal–organic framework based field effect chemical sensors: UiO-66-NH2 for nerve agent detection

L. Stassen, B. Bueken, H. Reinsch, J.F.M. Oudenhoven, D. Wouters, J. Hajek, V. Van Speybroeck, N. Stock, P.M. Vereecken, R. Van Schajik, D. De Vos, R. Ameloot
Chemical Science
7, 5827-5832
2016
A1

Abstract 

We present a highly sensitive gas detection approach for the infamous ‘nerve agent’ group of alkyl phosphonate compounds. Signal transduction is achieved by monitoring the work function shift of metal–organic framework UiO-66-NH2 coated electrodes upon exposure to ppb-level concentrations of a target simulant. Using the Kelvin probe technique, we demonstrate the potential of electrically insulating MOFs for integration in field effect devices such as ChemFETs: a three orders of magnitude improvement over previous work function-based detection of nerve agent simulants. Moreover, the signal is fully reversible both in dry and humid conditions, down to low ppb concentrations. Comprehensive investigation of the interactions that lead towards this high sensitivity points towards a series of confined interactions between the analyte and the pore interior of UiO-66-NH2.

Open Access version available at UGent repository

Acidity constant (pKa) calculation of large solvated dye molecules: evaluation of two advanced molecular dynamics methods

T. De Meyer, B. Ensing, S.M.J. Rogge, K. De Clerck, E.J. Meijer, V. Van Speybroeck
ChemPhysChem
17 (21), 3447–3459
2016
A1

Abstract 

pH-sensitive dyes are increasingly applied onto polymer substrates for the creation of novel sensor materials. Recently, these dye molecules have been modified to form a covalent bond with the polymer host. This can have a large influence on the pH-sensitive properties, in particular on the acidity constant (pKa). Obtaining molecular control over the factors that influence the pK$_a$ value is mandatory for future intelligent design of sensor materials. Herein, we show that advanced molecular dynamics (MD) methods have reached the level where pKa values of large solvated dye molecules can be predicted with high accuracy. Two MD methods are used in this work: steered or restrained MD and the insertion/deletion scheme. Both are first calibrated on a set of phenol derivatives and afterwards applied to the dye molecule Bromothymol Blue. Excellent agreement with experimental values is obtained, which opens perspectives for using these methods for designing dye molecules.

Open Access version available at UGent repository

Effect of temperature and branching on the nature and stability of alkene cracking intermediates in H-ZSM-5

P. Cnudde, K. De Wispelaere, J. Van der Mynsbrugge, M. Waroquier, V. Van Speybroeck
Journal of Catalysis
345, 53-69
2017
A1

Abstract 

Catalytic cracking of alkenes takes place at elevated temperatures in the order of 773–833 K. In this work, the nature of the reactive intermediates at typical reaction conditions is studied in H-ZSM-5 using a complementary set of modeling tools. Ab initio static and molecular dynamics simulations are performed on different C4single bond C5 alkene cracking intermediates to identify the reactive species in terms of temperature. At 323 K, the prevalent intermediates are linear alkoxides, alkene π-complexes and tertiary carbenium ions. At a typical cracking temperature of 773 K, however, both secondary and tertiary alkoxides are unlikely to exist in the zeolite channels. Instead, more stable carbenium ion intermediates are found. Branched tertiary carbenium ions are very stable, while linear carbenium ions are predicted to be metastable at high temperature. Our findings confirm that carbenium ions, rather than alkoxides, are reactive intermediates in catalytic alkene cracking at 773 K.

Open Access version available at UGent repository

Water coordination and dehydration processes in defective UiO-66 type metal organic frameworks

M. Vandichel, J. Hajek, A. Ghysels, A. De Vos, M. Waroquier, V. Van Speybroeck
CrystEngComm
18 (37), 7056-7069
2016
A1

Abstract 

The UiO-66 metal organic framework is one of the most thermally and chemically stable hybrid materials reported to date. However, it is also accepted that the material contains structurally embedded defects, which may be engineered to enhance properties towards specific applications such as catalysis, sensing, etc. The synthesis conditions determine to a large extent the level of perfection of the material and additionally the catalytic activity may be enhanced by post-synthesis activation at high temperature under vacuum, in which defect coordinating species (H2O, HCl, monocarboxylic modulators, etc.) evaporate. The molecular level characterization of defects is extremely challenging from both theoretical and experimental points of view. Such experimental endeavor was recently proposed via experimental SXRD measurements, also unraveling the coordination of water on the Zr–O–Zr defect sites [Angew. Chem., Int. Ed., 2015, 54, 11162–11167]. The present work provides a theoretical understanding of defect structures in UiO-66(Zr) by means of periodic density functional theory calculations and ab initio molecular dynamics simulations. A range of defect structures are generated with different numbers of missing linkers. For each of the defects, the free energetic and mechanical stability is discussed and the coordination of water and charge balancing hydroxide ions is studied. For catalysis applications, the material is mostly pretreated to remove water by dehydration reactions. For each of the proposed defect structures, mechanistic pathways for dehydration reactions of the Zr-bricks are determined employing nudged elastic band (NEB) calculations. During the dehydroxylation trajectory, loose hydroxyl groups and terephthalate decoordinations are observed. Furthermore, dehydration reactions are lower activated if terephthalate linkers are missing in the immediate environment of the inorganic brick. The creation of defects and the dehydration processes have a large impact on the mechanical properties of the material, which is evidenced by lower bulk moduli and elastic constants for structures with more defects.

DOI 

10.1039/C6CE01027J

Effect of Lewis acids on the stereoregularity of N,N-dimethyl acrylamide: A computational approach

T. Furuncuoğlu, B. Kura, S. Catak, H. Goossens, V. Van Speybroeck, M. Waroquier, V. Aviyente
European Polymer Journal
83, 67–76
2016
A1

Abstract 

In this study, the effect of Lewis acid coordination (ScCl3) in controlling the stereoregularity during the free radical polymerization of N,N-dimethyl acrylamide (DMAM) has been investigated by Density Functional Theory (DFT). Experimentally, ScCl3, Sc(OTf)3 and Yb(OTf)3 have been used to increase the isotactic percentage in the polymerization of another acrylamide derivative, N-isopropyl acrylamide (NIPAM) (Habaue et al., 2002). The relative orientation of the terminal and penultimate side chains is expected to determine the stereoregularity in free radical polymerization reactions (Noble et al., 2014). We have analyzed the mechanistic details of the propagation reaction by considering all coordination types of the Lewis acid to the propagating species. Calculations have shown the bridging of the Lewis acid between the terminal side chain and the monomer to be the most probable pathway, which is in favor of the pro-meso propagation during the free radical polymerization of DMAM. In this case, it is the bridging capacity of the catalyst along the less crowded direction that dictates the preference for isotacticity. Overall, the strategy suggested in this study can be easily used by experimentalists in their endeavour of choosing the catalysts in order to end-up with the desired stereoregulation of the polymer chain.

Heterogeneous Ru(III) oxidation catalysts via ‘click’ bidentate ligands on a Periodic Mesoporous Organosilica support

S. Clerick, E. De Canck, K. Hendrickx, V. Van Speybroeck, P. Van der Voort
Green Chemistry
18, 6035–6045
2016
A1

Abstract 

A 100% monoallyl ring-type Periodic Mesoporous Organosilica (PMO) is prepared as a novel, versatile and exceptionally stable catalytic support with a high internal surface area and 5.0 nm pores. Thiol-ene ‘click’ chemistry allows straightforward attachment of bifunctional thiols (-NH2, -OH, -SH) which, exploiting the thioether functionality formed, give rise to ‘solid’ bidentate ligands. [Ru(acac)2(CH3CN)2]PF6 is attached and complex formation on the solid is studied via theoretical calculations. All resulting solid catalysts show high activity and selectivity in alcohol oxidation reactions performed in green conditions (25°C/ water). The PMO catalysts do not leach Ru during reaction and are thus easily recuperated and re-used for several runs. Furthermore, oxidation of poorly water-soluble (±)-menthol illustrates the benefits of using hydrophobic PMOs as catalytic supports.

DMRG-CASPT2 study of the longitudinal static second hyperpolarizability of all-trans polyenes

S. Wouters, V. Van Speybroeck, D. Van Neck
Journal of Chemical Physics
145 (5), 054120
2016
A1

Abstract 

We have implemented internally contracted complete active space second order perturbation theory (CASPT2) with the density matrix renormalization group (DMRG) as active space solver [Y. Kurashige and T. Yanai, J. Chem. Phys. 135, 094104 (2011)]. Internally contracted CASPT2 requires to contract the generalized Fock matrix with the 4-particle reduced density matrix (4-RDM) of the reference wavefunction. The required 4-RDM elements can be obtained from 3-particle reduced density matrices (3-RDM) of different wavefunctions, formed by symmetry-conserving single-particle excitations op top of the reference wavefunction. In our spin-adapted DMRG code chemps2 [https://github.com/sebwouters/chemps2], we decompose these excited wavefunctions as spin-adapted matrix product states, and calculate their 3-RDM in order to obtain the required contraction of the generalized Fock matrix with the 4-RDM of the reference wavefunction. In this work, we study the longitudinal static second hyperpolarizability of all-trans polyenes C_{2n}H_{2n+2} [n = 4 - 12] in the cc-pVDZ basis set. DMRG-SCF and DMRG-CASPT2 yield substantially lower values and scaling with system size compared to RHF and MP2, respectively.

Minimal Basis Iterative Stockholder: Atoms-in-Molecules for Force-Field Development

T. Verstraelen, S. Vandenbrande, F. Heidar-Zadeh, L. Vanduyfhuys, V. Van Speybroeck, M. Waroquier, P.W. Ayers
Journal of Chemical Theory and Computation (JCTC)
12(8), 3894-3912
2016
A1

Abstract 

Atomic partial charges appear in the Coulomb term of many force-field models and can be derived from electronic structure calculations with a myriad of atoms-in-molecules (AIM) methods. More advanced models have also been proposed, using the distributed nature of the electron cloud and atomic multipoles. In this work, an electrostatic force field is defined through a concise approximation of the electron density, for which the Coulomb interaction is trivially evaluated. This approximate "pro-density" is expanded in a minimal basis of atom-centered s-type Slater density functions, whose parameters are optimized by minimizing the Kullback-Leibler divergence of the pro-density from a reference electron density, e.g. obtained from an electronic structure calculation. The proposed method, Minimal Basis Iterative Stockholder (MBIS), is a variant of the Hirshfeld AIM method but it can also be used as a density-fitting technique. An iterative algorithm to refine the pro-density is easily implemented with a linear-scaling computational cost, enabling applications to supramolecular systems. The benefits of the MBIS method are demonstrated with systematic applications to molecular databases and extended models of condensed phases. A comparison to 14 other AIM methods shows its effectiveness when modeling electrostatic interactions. MBIS is also suitable for rescaling atomic polarizabilities in the Tkatchenko-Sheffler scheme for dispersion interactions.

Exploring the flexibility of MIL-47(V)-type materials using force field molecular dynamics simulations

J. Wieme, L. Vanduyfhuys, S.M.J. Rogge, M. Waroquier, V. Van Speybroeck
Journal of Physical Chemistry C
120 (27), 14934-14947
2016
A1

Abstract 

The flexibility of three MIL-47(V)-type materials (MIL-47, COMOC-2 and COMOC-3) has been explored by constructing the pressure-versus-volume and free energy-versus-volume curves at various temperatures ranging from 100 K to 400 K. This is done with first-principles based force fields using the recently proposed QuickFF parameterization protocol. Specific terms were added for the materials at hand to describe the asymmetry of the one-dimensional vanadium-oxide chain and to account for the flexibility of the organic linkers. The force fields are used in a series of molecular dynamics simulations at fixed volumes, but varying unit cell shapes. The three materials show a distinct pressure-versus-volume behavior, which underlines the ability to tune the mechanical properties by varying the linkers towards different applications such as nanosprings, dampers and shock absorbers.

Open Access version available at UGent repository

Cutting the cost of carbon capture: a case for carbon capture and utilization

L. Joos, J. Huck, V. Van Speybroeck, B. Smit
Faraday Discussions
192, 391-414
2016
A1

Abstract 

A significant part of the cost for Carbon Capture and Storage (CCS) is related to the compression of the captured CO2 to its supercritical state, at 150 bar and typically 99% purity. These stringent conditions may however not always be necessary for specific cases of Carbon Capture and Utilization (CCU). In this manuscript, we investigate how much the parasitic energy of an adsorbent-based carbon capture process may be lowered by utilizing CO2 at 1 bar and adapting the final purity requirement for CO2 from 99% to 70% or 50%. We compare different CO2 sources: the flue gases of coal-fired or natural gas-fired power plants and ambient air. We evaluate the carbon capture performance of over 60 nanoporous materials and determine the influence of the initial and final purity on the parasitic energy of the carbon capture process. Moreover, we demonstrate the underlying principles of the parasitic energy minimization in more detail using the commercially available NaX zeolite. Finally, the calculated utilization cost of CO2 is compared with reported prices for CO2 and published costs for CCS.

Open Access version available at UGent repository

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