We present a new quantum mechanics/molecular mechanics (QM/MM) embedding approach for systems with directional polar covalent bonds. This “covalent elastic polarizable environment” (covEPE) scheme features a variational treatment of an energy expression that includes all degrees of freedom of both the QM region (the “cluster”) and the MM regions (the “environment”). The method completely and explicitly includes both the electrostatic and mechanical interactions between a QM model cluster and its environment. Monovalent pseudoatoms that represent real atoms of the material saturate the dangling bonds of the cluster; these pseudoatoms belong simultaneously to the QM and MM regions. For a correct description of a pure silica environment, we constructed a new force field of the shell-model type based on potential derived charges instead of formal charges. We implemented the covEPE approach in the density functional program ParaGauss and applied it to pure-silica and Al-containing chabazite, employing a generalized gradient approximation. These applications showed that calculated structural parameters and OH frequencies of bridging hydroxyl groups reproduce experimental data with good accuracy compared to other contemporary computational methods.

ABSTRACT:The parallel density functional program PARAGAUSS has been extended by a tool for computing solvent effects based on the conductor-like screening model (COSMO). The molecular cavity in the solvent is constructed as a set of overlapping spheres according to the GEPOL algorithm. The cavity tessellation scheme and the resulting set of point charges on the cavity surface comply with the point group symmetry of the solute. Symmetry is exploited to reduce the computational effort of the solvent model. To allow an automatic geometry optimization including solvent effects, care has been taken to avoid discontinuities due to the discretization (weights of tesserae, number of spheres created by GEPOL). In this context, an alternative definition for the grid points representing the tesserae is introduced. In addition to the COSMO model, short-range solvent effects are taken into account via a force field. We apply the solvent module to all-electron scalar-relativistic density functional calculations on uranyl, UO 2 2+ , and its aquo complexes in aqueous solution. Solvent effects on the geometry are very small. Based on the model [UO 2 (H 2 O) 5 ] 2+ , the solvation energy of uranyl is estimated to be about −400 kcal/mol, in agreement with the range of experimental data. The major part of the FUCHS, SHOR, AND RÖSCHsolvation energy, about −250 kcal/mol, is due to a donor-acceptor interaction associated with a coordination shell of five water ligands. One can interpret this large solvation energy also as a compounded effect of an effective reduction of the uranyl moiety plus a solvent polarization. The energetic effect of the structure relaxation in the solution is only about 8 kcal/mol.

The depletion of oxidized metal sulfide surfaces in metals due to the preferential release of cations is a common, but as yet poorly understood phenomenon. Herein, X-ray photoelectron spectroscopy using excitation energies from 1.25 keV to 6 keV, and Fe K- and S K-edge X-ray absorption near-edge spectra in total electron and partial fluorescence yield modes was employed to study natural chalcopyrite oxidized in air and etched in an acidic ferric sulfate solution. The metal-depleted undersurface formed was found to consist of a thin, 1-4 nm, outer layer containing polysulfide species, a layer with a pronounced deficiency of metals, mainly iron, and an abundant disulfide content but negligible polysulfide content (about 20 nm thick after the chemical etching), and a defective underlayer which extended down to about a hundred nm. DFT+U was used to simulate chalcopyrite with increasing numbers of removed Fe atoms. It was found that the structure with disulfide anion near double Fe vacancies, and the 'defective' structure comprising Cu in the position of Fe and Cu vacancy are most energetically favorable, especially when using a higher Hubbard-type parameter U, and have a large density of states at the Fermi level, whereas polysulfide anions are stable only near the surface. We propose a mechanism explaining the formation of the layered undersurface and 'passivation' of metal sulfides by (i) arrested decomposition of a nearly stoichiometric sulfide surface, and (ii) faster interfacial transfer and solid diffusion of cations towards the surface; (iii) stability limits for specific defect structures, promoting their expansion in depth rather than through compositional changes, excluding surface layers; (iv) decay of surface polysulfide layer yielding elemental sulfur.

We studied the preferential location of Ti centers in the framework of the Ti-containing MFI zeolite TS-1 using a hybrid DFT/MM embedding method developed recently. This "covalent elastic polarizable environment" (covEPE) cluster embedding allows a complete and self-consistent treatment of solid covalent systems such as zeolites. For the present study, we used a gradient-corrected density functional approach. The resulting structural features of both Si- and Ti-substituted forms of the zeolite framework fit well with available experimental information. The calculated substitution energy of Ti at the 12 crystallographically different tetrahedral sites of the MFI structure vary within 19 kJ/mol with T12 and T2 as most and least preferred sites, respectively. On the basis of these computational results and the preferential sites for Ti substitution reported from different experimental investigations, we concluded that the Ti distribution in the TS-1 framework is not governed by the thermodynamic stability of the pure material.