M. Waroquier

A Fourier-based method is presented to relate changes of the molecular structure during a molecular dynamics simulation with fluctuations in the electronic excitation energy. The method implies sampling of the ground state potential energy surface. Subsequently, the power spectrum of the velocities is compared with the power spectrum of the excitation energy computed using time-dependent density functional theory. Peaks in both spectra are compared, and motions exhibiting a linear or quadratic behavior can be distinguished. The quadratically active motions are mainly responsible for the changes in the excitation energy and hence cause shifts between the dynamic and static values of the spectral property. Moreover, information about the potential energy surface of various excited states can be obtained. The procedure is illustrated with three case studies. The first electronic excitation is explored in detail and dominant vibrational motions responsible for changes in the excitation energy are identified for ethylene, biphenyl, and hexamethylbenzene. The proposed method is also extended to other low-energy excitations. Finally, the vibrational fingerprint of the excitation energy of a more complex molecule, in particular the azo dye ethyl orange in a water environment, is analyzed.

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.

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.

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.

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.