Assessment methods for embedding schemes - Ceria as an example

The purpose of this paper is to present tests that are suitable to perform as an assessment of the quality of embedded-cluster models for ionic surfaces. Bulk and surface clusters of CeO₂ were constructed and the embedding quality was evaluated as a function of cluster size and stoichiometry. Out of the properties evaluated, it is found that the difference electron density (between the embedded cluster model and an equivalent periodic slab model), as well as the electrostatic potential above the surface are very sensitive to the embedding quality and can successfully be used as selection tools in the quality assessment. This was confirmed by subsequent CO₂ physisorption calculations for a number of embedded CeO₂(1 1 1) clusters.     

Oxygen vacancy formation for transient structures on the CeO2(110) surface at 300 and 750 K

Ab initio embedded-cluster calculations have been performed for the CeO2(110) surface using temperature induced structures from molecular dynamics (MD) snapshots. As a first step towards understanding how temperature induced distortions of the surface structure influence the surface oxygen reactivity, the energy cost of removing an O atom from the surface was calculated for 41 snapshots from the MD simulation at 300 K. The quantum mechanical embedded-cluster calculations show that already at 300 K the dynamics causes significant fluctuations (root mean square of 0.37 eV) in the O vacancy formation energy (Evac) while the distribution of the two excess electrons associated with the vacancy is virtually unaffected by the surface dynamics and remains localized on the two Ce ions close to the vacancy. It is also found that the quantum mechanical Evac fluctuations can be reproduced by oxygen vacancy calculations using only the relaxed shell-model force field (FF) itself and the MD geometries. Using the FF as the interaction model, the effect of raising the temperature to 750 K and the effect of doping with Ca were investigated for the oxygen vacancy formation.     

Coordination chemistry of the solvated silver(I) ion in the oxygen donor solvents water, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea

The hydrated and dimethyl sulfoxide and N,N'-dimethylpropyleneurea solvated silver(I) ions have been characterized structurally in solution by means of extended X-ray absorption fine structure (EXAFS) and large-angle X-ray scattering (LAXS). The coordination chemistry of the hydrated and dimethyl sulfoxide solvated silver(I) ions has been reevaluated because of different results from the EXAFS and LAXS methods reported previously. Consistent results are obtained with a linearly distorted tetrahedral model with two short and approximately two long Ag-O bond distances: mean Ag-O bond lengths of 2.32(1) and 2.54(1) A for the hydrate, 2.31(1) and 2.48(2) A for the dimethyl sulfoxide solvate, and 2.31(1) and 2.54(2) A for the N,N'-dimethylpropyleneurea solvate, in solution.     

Treatment of delocalized electron transfer in periodic and embedded cluster DFT calculations: The case of Cu on ZnO (10 0)

We assess the consequences of the interface model—embedded‐cluster or periodic‐slab model—on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic‐slab calculations indicate a delocalized charge‐transfer state. Our example is Cu atom adsorption on ZnO(10 0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded‐cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom‐centered and plane‐waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10 0), as long as care is taken to account for the effects of CT. © 2015 Wiley Periodicals, Inc.     

Structure and dynamics of water dangling OH bonds in hydrophobic hydration shells. Comparison of simulation and experiment

Molecular dynamics and electric field strength simulations are performed in order to quantify the structural, dynamic, and vibrational properties of non-H-bonded (dangling) OH groups in the hydration shell of neopentane, as well as in bulk water. The results are found to be in good agreement with the experimentally observed high-frequency (～3660 cm(-1)) OH band arising from the hydration shell of neopentanol dissolved in HOD/D(2)O, obtained by analyzing variable concentration Raman spectra using multivariate curve resolution (Raman-MCR). The simulation results further indicate that hydration shell dangling OH groups preferentially point toward the central carbon atom of neopentane to a degree that increases with the lifetime of the dangling OH.     

Surface properties of rutile TiO2(1 1 0) from molecular dynamics and lattice dynamics at 300 K: Variable-charge model results

Geometric structure, atomic vibrations and atomic charges and their thermally induced fluctuations have been calculated as a function of depth in, and thickness of, rutile TiO₂(1 1 0) slabs, within the framework of the variable-charge potential of Swamy and Gale [V. Swamy, J.D. Gale, Phys. Rev. B 62 (2000) 5406] at 300 K. Molecular dynamics simulations and lattice dynamics calculations were performed with a 2D periodic slab model for slab thicknesses between 3 and 11 triple layers (approximately 9-35 Å). Odd-even oscillations with respect to the number of slab layers are found for the surface relaxation for very thin slabs, and for the (slowly converging) rumpling in the middle of the slab. The Ti and O atomic charges in the outermost three atomic layers differ from the rest of the slab (they are less ionic); the thermal vibrations do not alter this picture. The atomic mean-square amplitudes are some 50% larger (more for O, less for Ti) at the surface than in the middle of the slab and decay rather slowly to the bulk values. Comparisons with the results of a rigid-ion potential for titania [M. Matsui, M. Akaogi, Mol. Simul. 6 (1991) 238] are presented for non-electronic properties.     

Comparison of methods for point‐charge representation of electrostatic fields

The calculation of the electrostatic potential resulting from an infinite or extended array of charges in the interior of a region of interest is a frequent task in computational chemistry. In case of a periodic potential this can, for example, be done by Ewald summation or by multipole methods. An important alternative are those methods where arrays of auxiliary point charges are optimized with respect to charge and/or position to reproduce the original electrostatic potential. In the literature different variations are reported. We compare the performance of some of these with respect to their ability to reproduce the original potential and the computational effort required. Between (1) surface charges determined by the conductor‐boundary condition, (2) optimized surface charges, and (3) surface charges floating on the surface we find that (2) offers good quality with small computational costs involved. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

On velocity scaling in molecular dynamics simulations

The effect of scaling the molecular velocities to a fixed total energy in molecular dynamics simulations within the (N,V,E) ensemble has been investigated. The effect of using different time steps is also discussed. It is found that, even for small time steps, velocity scaling has a substantial influence on the resulting molecular trajectories, velocities, and forces. Furthermore, velocity rescaling and larger time step seem to have an additive effect on the calculated trajectories, but not on the average thermodynamic properties, such as temperature, pressure, and energy.