T. Verstraelen

Computation of charge distribution and electrostatic potential in silicates with the use of chemical potential equalization models

T. Verstraelen, S.V. Sukhomlinov, V. Van Speybroeck, M. Waroquier, K. Smirnov
Journal of Physical Chemistry C
116 (1), 490–504
2012
A1

Abstract 

New parameters for the electronegativity equalization model (EEM) and the split-charge equilibration (SQE) model are calibrated for silicate materials, based on an extensive training set of representative isolated systems. In total, four calibrations are carried out, two for each model, either using iterative Hirshfeld (HI) charges or ESP grid data computed with Density Functional Theory (DFT) as a reference. Both the static (ground state) reference quantities and their responses to uniform electric fields are included in the fitting procedure. The EEM model fails to describe the response data, while the SQE model quantitatively reproduces all the training data. For the ESP-based parameters, we found that the reference ESP data are only useful at those grid points where the electron density is lower than 10-3 a.u. The density value correlates with a distance criterion used for selecting grid points in common ESP fitting schemes. All parameters are validated with DFT computations on an independent set of isolated systems (similar to the training set), and on a set of periodic systems including dense and microporous crystalline silica structures, zirconia, and zirconium silicate. Although the transferability of the parameters to new isolated systems poses no difficulties, the atomic hardness parameters in the HI-based models must be corrected to obtain accurate results for periodic systems. The SQE/ESP model permits the calculation of the ESP with similar accuracy in both isolated and periodic systems.

Open Access version available at UGent repository

Molecular dynamics study of the silica–water–SDA interactions

B.M. Szyja, A.P.J. Jansen, T. Verstraelen, R.A. van Santen
Physical Chemistry Chemical Physics (PCCP)
11 (35), 7605-7610
2009
A1

Abstract 

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.

Multi-level Modeling of Silica–Template Interactions During Initial Stages of Zeolite Synthesis

T. Verstraelen, B.M. Szyja, D. Lesthaeghe, R. Declerck, V. Van Speybroeck, M. Waroquier, A.P.J. Jansen, A. Aerts, L.R.A Follens, J.A. Martens, C. Kirschhock, R.A. van Santen
Topics in Catalysis
52 (9), 1261-1271
2009
A1

Abstract 

Zeolite synthesis is driven by structure-directing agents, such as tetrapropyl ammonium ions (TPA(+)) for Silicalite-1 and ZSM-5. However, the guiding role of these organic templates in the complex assembly to highly ordered frameworks remains unclear, limiting the prospects for advanced material synthesis. In this work, both static ab initio and dynamic classical modeling techniques are employed to provide insight into the interactions between TPA(+) and Silicalite-1 precursors. We find that as soon as the typical straight 10-ring channel of Silicalite-1 or ZSM-5 is formed from smaller oligomers, the TPA(+) template is partially squeezed out of the resulting cavity. Partial retention of the template in the cavity is, however, indispensable to prevent collapse of the channel and subsequent hydrolysis.

The electronegativity equalization method and the split charge equilibration applied to organic systems: Parametrization, validation, and comparison

T. Verstraelen, V. Van Speybroeck, M. Waroquier
Journal of Chemical Physics
131 (4), 044127
2009
A1

Abstract 

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.

MD-TRACKS: A Productive Solution for the Advanced Analysis of Molecular Dynamics and Monte Carlo simulations

T. Verstraelen, M. Van Houteghem, V. Van Speybroeck, M. Waroquier
Journal of Chemical Information and Modeling (JCIM)
48 (12), 2414–2424
2008
A1

Abstract 

In this paper, we present MD-TRACKS, an advanced statistical analysis toolkit for Molecular Dynamics and Monte Carlo simulations. The program is compatible with different molecular simulation codes, and the analysis results can be loaded into spreadsheet software and plotting tools. The analysis is performed with commands that operate on a binary trajectory database. These commands process not only plain trajectory data but also the output of other MD-TRACKS commands, which enables complex analysis work flows that are easily programmed in shell scripts. The applicability, capabilities, and ease of use of MD-TRACKS are illustrated by means of examples, that is, the construction of vibrational spectra and radial distribution functions from a molecular dynamics run is discussed in the case of tetrahydrofuran. These properties are compared with the experimental data available in the literature. MD-TRACKS is open-source software distributed at http://molmod.ugent.be/code/.

ZEOBUILDER: A GUI Toolkit for the Construction of Complex Molecular Structures on the Nanoscale with Building Blocks

T. Verstraelen, V. Van Speybroeck, M. Waroquier
Journal of Chemical Information and Modeling (JCIM)
48 ( 7), 1530-1541
2008
A1

Abstract 

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.

Temperature study of a glycine radical in the solid state adopting a DFT periodic approach: vibrational analysis and comparison with EPR experiments

E. Pauwels, T. Verstraelen, H. De Cooman, V. Van Speybroeck, M. Waroquier
Journal of Physical Chemistry B
112 (25), 7618-7630
2008
A1

Abstract 

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.

MFI Fingerprint: How Pentasil-Induced IR Bands Shift during Zeolite Nanogrowth

D. Lesthaeghe, P. Vansteenkiste, T. Verstraelen, A. Ghysels, C. Kirschhock, J.A. Martens, V. Van Speybroeck, M. Waroquier
Journal of Physical Chemistry C
112 (25), 9186-9191
2008
A1

Abstract 

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.

Effect of temperature on the EPR properties of a rhamnose alkoxy radical: A DFT molecular dynamics study

E. Pauwels, T. Verstraelen, M. Waroquier
Spectrochimica Acta Part A (Mol. & biomol.)
69 (5), 1388-1394
2008
A1

Abstract 

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.

Open Access version available at UGent repository

Calculating Reaction Rates with Partial Hessians: Validation of the Mobile Block Hessian Approach

A. Ghysels, V. Van Speybroeck, T. Verstraelen, D. Van Neck, M. Waroquier
Journal of Chemical Theory and Computation (JCTC)
4 (4) 614-625
2008
A1

Abstract 

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.

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