Heitor A. De Abreu

First-Principles Calculations and Electron Density Topological Analysis of Covellite (CuS)

Covellite (CuS) is an important mineral sulfide that can be used in many technological applications. It has a simple formula but a complex structure consisting of alternating layers of planar CuS3 triangles and CuS4 tetrahedrons with S-S bonds. Accurate first-principles calculations are performed for covellite structure (CuS), aiming to provide insights about its structural, mechanical and electronic properties and to unveil the nature of its chemical bonding. DFT and DFT+U methods have been used and showed to be sensitive to the correlation treatment (U value). Although it is not possible to extract a universal value of the U, this study indicates that U = 5 eV is an adequate value. The electronic structure analysis shows a significant metallic character due to p(S)-d(Cu) orbital interactions up to Fermi level. The projected density of states indicates that most of the contribution comes from the atomic orbitals in the [001] plane of the covellite, explaining the conductivity anisotropy observed experimentally. Topological analysis of the electron density was performed by means of quantum theory of atoms in molecules (QTAIM). Two different topological charges in Cu and S were calculated, confirming an ionic model with mix-charges. This mineral presents ionic degree of ∼ 32%. On the basis of the QTAIM analysis, the covalent character of S-S bond is confirmed, and the favored cleavage of CuS at the [001] surface might be at the Cu-S bond. The S atoms occupy most of the cell volume, and their contributions dominate the crystal compressibility: κ(S) ≈ κ(CuS).

Electronic and structural properties of bulk arsenopyrite and its cleavage surfaces – a DFT study

Arsenopyrite is the most abundant arsenic containing mineral on Earth and it is normally associated with many other minerals of economic importance. Therefore, it is involved in the environmental impacts of mining activities. The bonding nature of arsenopyrite and its preferential cleavage surface are still controversial. In the present work we have investigated the structural and electronic properties of arsenopyrite and its cleavage surface formation using a density functional/plane waves method. The quantum theory of atoms in molecules (QTAIM) and electron localization function (ELF) were applied for investigating the nature of the bonding in arsenopyrite. No evidence was found for Fe–Fe bonding in the bulk structure. The As–S bond has large covalent character and it is unexpected to be broken in the surface formation. The cleavage and surface energies have been calculated indicating that the (001) surface is the most favored.

Solid-state experimental and theoretical investigation of the ammonium salt of croconate violet, a pseudo-oxocarbon ion.

The present work describes the crystal structure, vibrational spectra, and theoretical calculations of ammonium salts of 3,5-bis-(dicyanomethylene)cyclopentane-1,2,4-trionate, (NH(4))(2)(C(11)N(4)O(3)) [(NH(4))(2)CV], also known as ammonium croconate violet. This compound crystallizes in triclinic P1 and contains two water molecules per unit formula. The crystal packing is stabilized by hydrogen bonds involving water molecules and ammonium cations, giving rise to a 3D polymeric arrangement. In this structure, a pi-stacking interaction is not observed, as the smaller centroid-centroid distance is 4.35 A. Ab initio electronic structure calculations under periodic boundary conditions were performed to predict vibrational and electronic properties. The vibrational analysis was used to assist the assignments of the Raman and infrared bands. The solid structure was optimized and characterized as a minimum in the potential-energy surface. The stabilizing intermolecular hydrogen bonds in the crystal structure were characterized by difference charge-density analysis. The analysis of the density of states of (NH(4))(2)CV gives an energy gap of 1.4 eV with a significant contribution of carbon and nitrogen 2p states for valence and conduction bands.

Comparação estrutural entre amostras de materiais tipo hidrotalcita obtidas a partir de diferentes rotas de síntese

Three samples of hydrotalcite-like materials (HTC) were synthesized and their structural characteristics were compared with two HTCs obtained commercially. Thermal analyses, FT-IR, PXRD and textural analyses were used to investigate the structural differences between commercial and synthetic samples. Particularly, the memory effect was observed at temperature higher than 600 oC. The Rietveld refinements were obtained with expressive accuracy and the statistical parameters of goodness of fit are quite satisfactory. In conclusion, the procedures adopted in synthesis of HTC produced crystalline materials with high surface area materials.

1,2,3- and 1,2,4-Benzenetricarboxylic ligands: investigation of unusual 2D and 3D polymeric nets with potassium ion

The present work presents a description of two unusual polymeric nets containing potassium (I) and benzenetricarboxylic ligand with formula [K(C9H5O6)·H2O] (1) and [K(C9H5O6)·(H2O)2] (2). Their structures were solved by single crystal X-ray diffraction methods. The structural results suggest that the interactions between carboxylate groups and potassium ion have an ionic character and they are similar for both compounds. The study of the chemical bond between the oxygen and potassium atoms was performed for compound 2 through density functional theory calculations and confirmed that compound 2 is stabilized by ionic interactions, which can be associated analogously to compound 1. The organization of these interactions into crystal packing was investigated by program package TOPOS4.0. It was found that these interactions play an important role in the construction of the 3D and 2D polymeric net for both compounds.

Isonicotinohydrazide conformation in a supramolecular system with 1,4-benzenedicarboxylic acid and Zn2+ and Mn2+

An anti-tuberculosis drug, isonicotinohydrazide (INH), is studied concerning its conformation in different crystalline environments. In the present work, compounds with zinc (1) and manganese (2) ions are reported where INH has different conformations, caused by hydrogen bonds with 1,4-benzenedicarboxylic acid (H2BDC) and water molecules and by coordination bonds involving its functional groups. In 1, INH is coordinated to two zinc ions, where H2BDC and crystallization water molecules form several hydrogen bonds giving rise to a complex three-dimensional (3-D) network. In 2, both INH and H2BDC molecules are coordinated to manganese as well as four water molecules. The complex formed interacts by hydrogen bonds forming a 2-D arrangement. A 3-D network extension arises from other hydrogen bonds generated by crystallization water. In these two compounds, the presence of BDC ion and water molecules is very important in the stabilization of the complexes and in INH conformation. This work is focused on the structural description of formed compounds.

Modeling the oxidation mechanism of pyrite and arsenopyrite – connection to acid rock drainage

Acid rock drainage (ARD) is hazardous to the environment and it is caused by the oxidation of sulfide minerals leading to the formation of acids and, consequently, enhancing the dissolution of the rocks. Therefore, ARD leads to the acidification of aquifers and mobilization of heavy metals in the environment. Sulfide minerals are the main source of noble metals such as copper and gold (besides zinc and lead), hence, ARD is the main environmental concern in the mining regions. Arsenopyrite is normally associated to other sulfide minerals. Its presence enhances the environmental problem since the poisoning arsenic is also released in the environment due to ARD phenomenon. In this chapter, the contribution of the computer modeling to the understanding of the oxidation mechanism of sulfide minerals is reviewed. The challenge for modeling such a complex reaction involving water and oxygen is highlighted. The effects of the pyrite/arsenopyrite interface to their oxidation mechanism are also discussed in the light of the recent reports.

Natural Organic Acid as Green Catalyst for Xanthenones Synthesis: Methodology, Mechanism and Calcium Channel Blocking Activity

Xanthenones were synthesized via one-pot tricomponent reaction, under solvent-free conditions, using aldehydes, phenolic and cyclic 1,3-dicarbonyl compounds. Natural organic acids (NOAs), compounds present in many living metabolisms, were used as potential green catalysts. NOA are considered to be more eco-friendly and user-friendly alternative to traditional methodologies. Optimization studies showed that oxalic acid was the best NOA catalyst for such reaction furnishing the xanthenones with up to 93% of yield. Theoretical calculations were performed to evaluate this reaction mechanism and regioselectivity. The results showed that the regiospecificity of this three-component reaction is kinetically and thermodynamically controlled by the addition of b-naphthol C2, instead of C10, to the aldehyde. Our results also disclosed two xanthenones as novel calcium channels blockers. Eco-friendly reaction conditions, easy workup procedure, short reaction times and good yields are some of the advantages of our methodology.

Structural, Electronic, and Thermodynamic Properties of the T and B Phases of Niobia: First-Principle Calculations

Different polymorphs of Nb2O5 can be obtained depending on the pressure and temperature of calcination leading to different catalytic properties. Two polymorphs of niobia, T-Nb2O5 and B-Nb2O5, have been investigated by means of density functional/plane waves method. The equation of state predicted that B-Nb2O5 phase is more stable than the T-Nb2O5 at low temperature; however at high pressure both phases are stable. These results are in good agreement with the available experimental data. The calculated cohesive energies of 6.63 and 6.59 eV·atom-1 for the B-Nb2O5 and T-Nb2O5, respectively, also corroborate this conclusion, and it can be compared to the experimental value of 9.56 eV atom-1 estimated for the most thermodynamically stable phase. The topological analyses based on quantum theory of atoms in molecules (QTAIM) and electron localization function (ELF) were applied and reveal bonds with large ionic character for both phases. The B-Nb2O5 presented larger stiffness than T-Nb2O5, and the oxygen sites in the T-Nb2O5 are more compressible. The density of states comparison for both structures indicates that B-Nb2O5 has lower concentration of acid sites compared to T-Nb2O5. This result is consistent with the experimental observations that the concentration of Lewis acid sites decreases with the temperature.

Chapter 6:Surface reactivity of the sulfide minerals

Mineral and mining industries have been associated to environmental degradation and natural resources exploration. The hazardous acid mining drainage (AMD), usually caused by the exposition of sulfide minerals to the environment, is of great importance, responsible for acidifying aquifers and releasing heavy metals, hence affecting all biota living around it. AMD is caused by oxidation of sulfide minerals when exposed to the oxidant environment leading to the sulfate formation. The intricate oxidation mechanism is a subject of intense research. Recently, density functional methods have been applied to investigate the reactivity of the sulfide minerals towards their oxidation. On the other hand, the understanding of the leaching mechanism of chalcopyrite is also of technological importance since this mineral is the main source of copper in the world. In the present chapter, different methodologies in the DFT framework applied to study sulfide minerals are reviewed. Recent publications about the reconstruction of the surfaces, surface energies, adsorption processes and reaction mechanisms of the pyrite, arsenopyrite and chalcopyrite using different DFT approaches are discussed. Experimental evidences that support the theoretical results have also been presented. The importance of the development of molecular modeling approaches that permit the investigation of the mineral/water interface is strengthened in the present chapter.