T. Verstraelen

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.

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/.

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.