Tomáš Bučko

Improved Description of the Structure of Molecular and Layered Crystals: Ab Initio DFT Calculations with van der Waals Corrections

The implementation of technique for full structural optimizations of complex periodic systems in the DFT-PAW package VASP, including the volume and shape of the unit cell and the internal coordinates of the atoms, together with a correction that allows an appropriate modeling of London dispersion forces, as given by the DFT-D2 approach of Grimme [Grimme, S. J. Comp. Chem. 2006, 27, 1787], is reported. Dispersion corrections are calculated not only for the forces acting on the atoms, but also for the stresses on the unit cell. This permits a simultaneous optimization of all degrees of freedom. Benchmark results on a series of prototype systems are presented and compared to results obtained by other methods and experimental data. It is demonstrated that the computationally inexpensive DFT-D2 scheme yields reasonable predictions for the structure, bulk moduli, and cohesive energies of weakly bonded materials.

Assessment of ten DFT methods in predicting structures of sheet silicates: Importance of dispersion corrections

The performance of ten density functional theory (DFT) methods in a prediction of the structure of four clay minerals, in which non-bonding interactions dominate in the layer stacking (dispersive forces in talc and pyrophyllite, and hydrogen bonds in lizardite and kaolinite), is reported. In a set of DFT methods following functionals were included: standard local and semi-local (LDA, PW91, PBE, and RPBE), dispersion corrected (PW91-D2, PBE-D2, RPBE-D2, and vdW-TS), and functionals developed specifically for solids and solid surfaces (PBEsol and AM05). We have shown that the standard DFT functionals fail in the correct prediction of the structural parameters, for which non-bonding interactions are important. The remarkable improvement leading to very good agreement with experimental structures is achieved if the dispersion corrections are included in the DFT calculations. In such cases the relative error for the most sensitive lattice vector c dropped below 1%. Very good performance was also observed for both DFT functionals developed for solids. Especially, the results achieved with the PBEsol are qualitatively similar to those with DFT-D2.

Improved Density Dependent Correction for the Description of London Dispersion Forces.

The Tkatchenko-Scheffler method for calculating dispersion correction to standard density-functional theory, which uses fixed neutral atoms as a reference to estimate the effective volumes of atoms-in-molecule and to calibrate their polarizabilities and dispersion coefficients, fails to describe the structure and the energetics of ionic solids. Here, we propose a more appropriate partitioning, based on the iterative Hirshfeld scheme, where the fractionally charged atomic reference state is determined self-consistently. We show that our new method extends the applicability of the original method in particular to study ionic systems and adsorption phenomena on surfaces of ionic solids.

Extending the applicability of the Tkatchenko-Scheffler dispersion correction via iterative Hirshfeld partitioning

Recently we have demonstrated that the applicability of the Tkatchenko-Scheffler (TS) method for calculating dispersion corrections to density-functional theory can be extended to ionic systems if the Hirshfeld method for estimating effective volumes and charges of atoms in molecules or solids (AIMs) is replaced by its iterative variant [T. Bučko, S. Lebègue, J. Hafner, and J. Ángyán, J. Chem. Theory Comput. 9, 4293 (2013)]. The standard Hirshfeld method uses neutral atoms as a reference, whereas in the iterative Hirshfeld (HI) scheme the fractionally charged atomic reference states are determined self-consistently. We show that the HI method predicts more realistic AIM charges and that the TS/HI approach leads to polarizabilities and C6 dispersion coefficients in ionic or partially ionic systems which are, as expected, larger for anions than for cations (in contrast to the conventional TS method). For crystalline materials, the new algorithm predicts polarizabilities per unit cell in better agreement with the values derived from the Clausius-Mosotti equation. The applicability of the TS/HI method has been tested for a wide variety of molecular and solid-state systems. It is demonstrated that for systems dominated by covalent interactions and/or dispersion forces the TS/HI method leads to the same results as the conventional TS approach. The difference between the TS/HI and TS approaches increases with increasing ionicity. A detailed comparison is presented for isoelectronic series of octet compounds, layered crystals, complex intermetallic compounds, and hydrides, and for crystals built of molecules or containing molecular anions. It is demonstrated that only the TS/HI method leads to accurate results for systems where both electrostatic and dispersion interactions are important, as illustrated for Li-intercalated graphite and for molecular adsorption on the surfaces in ionic solids and in the cavities of zeolites.

A density-functional study of the adsorption of methane-thiol on the (111) surfaces of the Ni-group metals: II. Vibrational spectroscopy

The vibrational eigenstates of methane-thiol (CH(3)SH) and methane-thiolate (CH(3)S) in the gas phase and in dense monolayers adsorbed on the (111) surfaces of the Ni-group metals have been investigated within the framework of density-functional theory using generalized response and force-constant techniques. For isolated CH(3)SH good agreement of eigenfrequencies and intensities with the measured infrared spectra is achieved. For the CH(3)S radical, experimental information from laser-induced fluorescence spectroscopy is available only for selected eigenmodes. The theoretical predictions show reasonable agreement for the C-H deformation and C-S stretching modes, but predict much higher C-H stretching frequencies in better agreement with estimates based on the vibrational fine structure of the photoemission spectra. For methane-thiol monolayers on Ni(111) and Pt(111) the calculations predict stronger red-shifts of the S-H and C-S stretching modes than reported from high-resolution electron energy loss spectroscopy (HREELS) on condensed multilayers which average over the first layer adsorbed on the metal and further physisorbed molecular layers. For methane-thiolate monolayers the calculations predict modest blue-shifts of the C-H stretching and rocking modes and for the asymmetric C-H deformation modes. Red-shifts are predicted for the symmetric C-H deformation and for the C-S stretching modes. Reasonable agreement with HREELS is achieved. The increased differences between symmetric and asymmetric C-H stretching and deformation modes induced by the adsorption is a consequence of the strongly tilted adsorption geometries.

Mechanism of alkane dehydrogenation catalyzed by acidic zeolites: Ab initio transition path sampling

The dehydrogenation of propane over acidic chabazite has been studied using ab initio density-functional simulations in combination with static transition-state searches and dynamic transition path sampling (TPS) methods at elevated temperatures. The acidic zeolite has been modeled both using a small cluster and a large periodic model consisting of two unit cells, the TPS simulations allow to account for the effect of temperature and entropy. In agreement with experimental observations we find propene as the dominant reaction product and that the barrier for the dehydrogenation of a methyl group is higher than that for a methylene group. However, whereas all studies based on small cluster models (including the present one) conclude that the reaction proceeds via the formation of an alkoxy intermediate, our TPS studies based on a large periodic model lead to the conclusion that propene formation occurs via the formation of various forms of propyl cations stabilized by entropy, while the formation of an alkoxy species is a relatively rare event. It was observed only in 15% of the reactive trajectories for methyl dehydrogenation and even in only 8% of the methylene dehydrogenation reactions. Our studies demonstrate the importance of entropic effects and the need to account for the structure and flexibility of the zeolitic framework by using large periodic models.

Many-body dispersion corrections for periodic systems: an efficient reciprocal space implementation

The energy and gradient expressions for the many-body dispersion scheme (MBD@rsSCS) of Ambrosetti et al (2014 J. Chem. Phys. 140 18A508) needed for an efficient implementation of the method for systems under periodic boundary conditions are reported. The energy is expressed as a sum of contributions from points sampled in the first Brillouin zone, in close analogy with planewave implementations of the RPA method for electrons in the dielectric matrix formulation. By avoiding the handling of large supercells, considerable computational savings can be achieved for materials with small and medium sized unit cells. The new implementation has been tested and used for geometry optimization and energy calculations of inorganic and molecular crystals, and layered materials.

Acid-based Catalysis in Zeolites Investigated by Density-Functional Methods

Zeolites are a unique class of microporous aluminosilicates with multiple applications as molecular sieves, detergents, desiccants and acid catalysts. Their catalytic activity is determined by Brønsted and Lewis acid sites created by protonation or activation by metallic cations. The reactivity of the acid sites is strongly influenced by the geometry and the flexibility of the zeolitic framework. Recent investigations of the reactivity of zeolites and simulations of catalytic reactions based on periodic-density-functional calculations are reviewed.

Ab initio study of structure and interconversion of native cellulose phases.

Dispersion-interaction corrected DFT simulations are performed to study the structure of two allomorphs of native cellulose I. Good agreement between theoretical and experimental data is achieved. Two H-bond patterns, previously identified experimentally, are examined for both allomorphs. The transition mechanism for the conversion between the phase I(α) and I(β) is studied by means of constrained relaxations. New metastable intermediate phase occurring on the I(α) → I(β) route is identified, and the corresponding structural data are reported.

Ab initio density functional investigation of the (001) surface of mordenite

Structural and acidic properties of the (001) surface of mordenite have been studied using density functional theory including generalized gradient corrections to the exchange-correlation functional. Our calculations, in agreement with experimental results, show that the surface structure of mordenite differs only moderately from the bulk structure, no reconstruction of the surface has been found. Part of the terminal silanol groups form weak hydrogen bonds with other framework oxygen sites, the lengths of hydrogen bonds vary in the range 1.9–2.6 A depending on the position of the Al site. The OH-stretching frequencies for various acid sites in the mordenite framework have been calculated. In agreement with experiment, calculated OH-stretching frequencies of terminal silanol groups are shifted by about 100 cm−1 with respect to the Bronsted acid sites. Those silanol groups whose OH-stretching frequencies are modified by the presence of hydrogen bonds are shown to absorb in the region typical for the Bronst...