T. Verstraelen

In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species and tetrapropylammonium ions/water evolve during the formation of the larger aggregates, that show initial micropore formation from more elementary building blocks. We have followed the dynamics and changes in the position of the tetrapropylammonium ions into the formation of TPA-Si22 complexes. Moreover, the analysis based on the geometries of the systems being studied as well as the radial distribution function allowed us to predict the location of the TPA cations in fully formed nanoslabs. An interesting result is reported that the template cannot be accommodated any more in the newly formed cavities, but is pushed out of the channel like cavities to positions where in a later stage channel cross sections can be formed.

An extensive benchmark of the electronegativity equalization method (EEM) and the split charge equilibration (SQE) model on a very diverse set of organic molecules is presented. These models efficiently compute atomic partial charges and are used in the development of polarizable force fields. The predicted partial charges that depend on empirical parameters are calibrated to reproduce results from quantum mechanical calculations. Recently, SQE is presented as an extension of the EEM to obtain the correct size dependence of the molecular polarizability. In this work, 12 parametrization protocols are applied to each model and the optimal parameters are benchmarked systematically. The training data for the empirical parameters comprise of MP2/Aug-CC-pVDZ calculations on 500 organic molecules containing the elements H, C, N, O, F, S, Cl, and Br. These molecules have been selected by an ingenious and autonomous protocol from an initial set of almost 500 000 small organic molecules. It is clear that the SQE model outperforms the EEM in all benchmark assessments. When using Hirshfeld-I charges for the calibration, the SQE model optimally reproduces the molecular electrostatic potential from the ab initio calculations. Applications on chain molecules, i.e., alkanes, alkenes, and alpha alanine helices, confirm that the EEM gives rise to a divergent behavior for the polarizability, while the SQE model shows the correct trends. We conclude that the SQE model is an essential component of a polarizable force field, showing several advantages over the original EEM.

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.

Silicalite-1 zeolite exhibits a characteristic pentasil framework vibration around 540−550 cm−1. In the initial stages of zeolite synthesis, however, this band is observed at much higher wavenumbers: literature shows this vibration to depend on particle size and to shift over 100 cm−1 with increasing condensation. In this work, the pentasil vibration frequency was derived from theoretical molecular dynamics simulations to obtain the correct IR band assignments for important nanoparticles. The IR spectroscopic fingerprint of oligomeric five-ring containing precursors proposed in the literature was computed and compared with experimental data. Our theoretical results show that, while isolated five-membered rings show characteristic vibrational bands around 650 cm−1, the combination of five-membered rings in the full MFI-type structure readily generates the bathochromic shift to the typical pentasil vibration around 550 cm−1. As opposed to what was previously believed, the IR band does not shift gradually as nanoparticle size increases, but it is highly dependent on the specific way structural units are added. The most important feature is the appearance of an additional band when double five-membered rings are included, which allows for a clear distinction between the key stages of early zeolite nucleation. Furthermore, the combination of the simulated spectra with the experimental observation of this spectral feature in nanoparticles extracted from silicalite-1 clear solutions supports their structured nature. The theoretical insights on the dependency of pentasil vibrations with the degree of condensation offer valuable support toward future investigations on the genesis of a zeolite crystal.

In an earlier paper, the authors have developed a new method, the mobile block Hessian (MBH), to accurately calculate vibrational modes for partially optimized molecular structures [J. Chem. Phys. 2007, 126 (22), 224102]. The proposed procedure remedies the artifact of imaginary frequencies, occurring in standard frequency calculations, when parts of the molecular system are optimized at different levels of theory. Frequencies are an essential ingredient in predicting reaction rate coefficients due to their input in the vibrational partition functions. The question arises whether the MBH method is able to describe the chemical reaction kinetics in an accurate way in large molecular systems where a full quantum chemical treatment at a reasonably high level of theory is unfeasible due to computational constraints. In this work, such a validation is tested in depth. The MBH method opens a lot of perspectives in predicting accurate kinetic parameters in chemical reactions where the standard full Hessian procedure fails.