M. Waroquier

The growth of polycyclic aromatic hydrocarbons (PAHs) is in many areas of combustion and pyrolysis of hydrocarbons an inconvenient side effect that warrants an extensive investigation of the underlying reaction mechanism, which is known to be a cascade of radical reactions. Herein, the focus lies on one of the key reaction classes within the coke formation process: hydrogen abstraction reactions induced by a methyl radical from methylated benzenoid species. It has been shown previously that hydrogen abstractions determine the global PAH formation rate. In particular, the influence of the polyaromatic environment on the thermodynamic and kinetic properties is the subject of a thorough exploration. Reaction enthalpies at 298 K, reaction barriers at 0 K, rate constants, and kinetic parameters (within the temperature interval 700–1100 K) are calculated by using B3LYP/6-31+G(d,p) geometries and BMK/6-311+G(3df,2p) single-point energies. This level of theory has been validated with available experimental data for the abstraction at toluene. The enhanced stability of the product benzylic radicals and its influence on the reaction enthalpies is highlighted. Corrections for tunneling effects and hindered (or free) rotations of the methyl group are taken into account. The largest spreading in thermochemical and kinetic data is observed in the series of linear acenes, and a normal reactivity–enthalpy relationship is obtained. The abstraction of a methyl hydrogen atom at one of the center rings of large methylated acenes is largely preferred. Geometrical and electronic aspects lie at the basis of this striking feature. Comparison with hydrogen abstractions leading to arylic radicals is also made.

During the synthesis of tricyclic phosphonopyrrolidines via intramolecular Diels−Alder reactions of 1-acylamino(furan-2-yl)methyl phosphonates, two isomers are formed in most cases. The presence of a short three-atom tether together with spectroscopic data, including difference NOE, revealed that the cycloaddition occurred exo, but the phosphonate substituent on the tether had an exo or endo orientation. This was confirmed via X-ray analysis. A thermodynamic preference for the product with the phosphonate function in the endo position was observed experimentally and was confirmed theoretically. Density functional theory methods and several high-level post Hartree−Fock procedures were used to rationalize the observed isomer ratio of the IMDAF-reactions. This was done for two different types of reagents: with the activating carbonyl group in the tether or as a substituent on the tether. For the first type of molecules there is a large steric hindrance of the bulky tether substituents that disfavors the exo-isomer. In the latter case, there was a very small energy difference between the transition states causing a mixture of epimers being formed.

In this paper, a new graphical toolkit, ZEOBUILDER, is presented for the construction of the most complex zeolite structures based on building blocks. Molecular simulations starting from these model structures give novel insights in the synthesis mechanisms of micro- and mesoporous materials. ZEOBUILDER is presented as an open-source code with easy plug-in facilities. This architecture offers an ideal platform for further development of new features. Another specific aspect in the architecture of ZEOBUILDER is the data structure with multiple reference frames in which molecules and molecular building blocks are placed and which are hierarchically ordered. The main properties of ZEOBUILDER are the feasibility for constructing complex structures, extensibility, and transferability. The application field of ZEOBUILDER is not limited to zeolite science but easily extended to the construction of other complex (bio)molecular systems. ZEOBUILDER is a unique user-friendly GUI toolkit with advanced plug-ins allowing the construction of the most complex molecular structures, which can be used as input for all ab initio and molecular mechanics program packages.

The major radiation-induced radical in crystalline glycine is examined using DFT calculations, in which both molecular environment and temperature are accounted for. This is achieved by molecular dynamics simulations of the radical embedded in a supercell under periodic boundary conditions. At 100 and 300 K, a vibrational analysis is performed based on Fourier transformation of the atomic velocity autocorrelation functions. By the use of a novel band-pass filtering approach, several vibrational modes are identified and associated with experimental infrared and Raman assignments. Decomposition of the calculated spectra in terms of radical motion reveals that several vibrational modes are unique to the radical, the most prominent one at 702 cm(-1) corresponding to out-of-plane motion of the paramagnetic center, inversely coupled with similar motion of the carboxyl carbon. A hybrid periodic/cluster scheme is used to evaluate the EPR properties of the glycine radical along the MD trajectories resulting in temperature dependent magnetic properties. These are compared with available experimental data conducted at 77 K and room temperature. Ground state or low temperature calculations yield very good agreement with 77 K experimental EPR properties. From the 300 K simulations, an important improvement is achieved on the isotropic hyperfine coupling of the (13)C tensor, which becomes closer to the value measured at room temperature. It is established that this is the result of a nonlinear relation between the planarity of the radical center and the isotropic couplings of the nuclei bound to it. Finally, a critical reevaluation of the experimental (14)N hyperfine tensor data strongly suggests that an erroneous tensor was reported in literature. It is convincingly shown that from the same experimental data set a different tensor can be derived, which is in substantially better agreement with all calculations.

It has been shown previously that two distinctive variants (called RHop and RO4) exist of the radiation-induced rhamnose alkoxy radical. Density functional theory (DFT) calculations of the electron paramagnetic resonance (EPR) properties were found to be consistent with two separate measurements at different temperatures [E. Pauwels, R. Declerck, V. Van Speybroeck, M. Waroquier, Radiat. Res., in press]. However, the agreement between theory and experiment was only of a qualitative nature, especially for the latter radical. In the present work, it is examined whether this residual difference between theoretical and experimental spectroscopic properties can be explained by explicitly accounting for temperature in DFT calculations. With the aid of ab-initio molecular dynamics, a temperature simulation was conducted of the RO4 variant of the rhamnose alkoxy radical. At several points along the MD trajectory, g and hyperfine tensors were calculated, yielding time (and temperature) dependent mean spectroscopic properties. The effect of including temperature is evaluated but found to be within computational error.