The crystal structures of a large number of silica polytypes (α-and β-quartz, α-and βcristobalite, β-tridymite, keatite, coesite and stishovite) have been studied using density functional theory, both in the local density approximation and including generalized-gradient corrections to the exchange-correlation functional. All crystal structures have been optimized by minimizing the total energy with respect to all lattice parameters and to the atomic coordinates within the unit cell (up to 40 structural parameters in the case of coesite). The α → β transitions in quartz and cristobalite have been studied in detail, including different variants proposed for the structure of βcristobalite. The tetragonal (I42d) and simple cubic (P 2 1 3) structures are found to be energetically almost degenerate near the equilibrium volume. On volume expansion both structures converge towards the idealized highly symmetric F d3m structure. A similar continuous transition from a more compact orthorhombic (C222 1) to a highly symmetric hexagonal (P 6 3 /mmc) variant is also proposed for β-tridymite. For coesite two monoclinic variants (with C2/c and P 2 1 /c spacegroup symmetries, respectively) have been examined and found to be energetically degenerate to within 1 meV per SiO 2 unit. It is shown that within the local density approximation (LDA) the equilibrium atomic volume of all polytypes is predicted with an accuracy better than one per cent. The LDA also leads to excellent structural predictions and to accurate values of the bulk modulus. Corrections in the framework of the generalized-gradient approximation (GGA) lead to substantially larger equilibrium volumes, although at fixed volume the LDA and GGA lead to identical crystal structures. The increased volume also leads to less accurate structural parameters. However, we find that gradient corrections are essential for achieving accurate structural energy differences between the tetrahedrally coordinated phases found at larger atomic volumes (all polytypes except stishovite) and the octahedrally coordinated high-pressure polymorphs (stishovite and post-stishovite phases).
Recent neutron-diffraction experiments revealed the presence of hydroxonium ions in the hydrated HSAPO-34, an aluminophosphate type zeolitic material, structurally isotypic with chabazite. Ab initio molecular dynamics (AIMD) simulations were used to decide whether the proton transfer from a Brønsted acid site to a single water molecule is possible in this material, or the simultaneous presence of two water molecules in the zeolite cage is necessary to realize such a transfer. The molecular dynamics calculations support the view that while the intrinsic acidity of the Brønsted site in HSAPO-34 is insufficient to protonate an isolated water molecule, the basicity of a hydrogen-bonded water dimer is high enough to act as proton acceptor at the acid site.
In this paper we report structural and energetic data for cysteine and selenocysteine in the gas phase and the effect of Co(2+) complexation on their properties. Different conformers are analyzed at the DFT/B3LYP level of both bound and unbound species. Geometries, vibrational frequencies, and natural population analysis are reported and used to understand the activity of these species. In particular, we have focused our attention on the role of sulfur and selenium in the metal binding process and on the resulting deprotonation of the thiol and seleniol functions. From the present calculations we are able to explain, both from electronic structure and thermochemical point of views, a metal-induced thiol deprotonation as observed in gas-phase experiments. A similar process is expected in the case of selenocysteine. In fact, cobalt was found to have a preferential affinity with respect to thiolate and selenolate functions. This can be related to the observation that only S and Se are able-in thiolate and selenolate states-to make a partial charge transfer to the cobalt thus forming very stable complexes. Globally, very similar results are found when substituting S with Se, and a very small difference in cobalt binding affinity is found, thus justifying the use of this substitution in X-ray absorption experiments done on biomolecules containing cysteine metal binding pockets.
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