Experimental and computational studies of crystal violet removal from aqueous solution using sulfonated graphene oxide.

Positively charged contaminants can be strongly attracted by sulfanilic acid-functionalized graphene oxide. Here, sulfonated graphene oxide (GO-SO3H) was synthesized and characterized for cationic crystal violet (CV) adsorption. We further studied the effect of pH, initial concentration, and temperature on CV uptake. The highest CV uptake occurred at pH 8. A kinetic study was also carried out by applying the pseudo-first-order and pseudo-second-order models. The pseudo-second-order's adsorption capacity (qe) value was much closer to the experimental qe (qeexp:0.13, qecal:0.12) than the pseudo-first-order model (qeexp:0.13, qecal:0.05). The adsorption performance was accomplished rapidly since the adsorption equilibrium was closely obtained within 30 min. Furthermore, the adsorption capacity was significantly increased from 42.85 to 79.23%. The maximum adsorption capacities of GO-SO3H where 97.65, 202.5, and 196.2 mg·g-1 for CV removal at 298, 308, and 328 K, respectively. The Langmuir and Freundlich adsorption isotherms were applied to the experimental data. The data fit well into Langmuir and Freundlich except at 298 K, where only Langmuir isotherm was most suitable. Thermodynamic studies established that the adsorption was spontaneous and endothermic. The adsorption mechanism was revealed by combining experimental and computational methods. These findings suggest that GO-SO3H is a highly adsorbent for removing harmful cationic dye from aqueous media.

Growing Mechanism of Polysulfides and Elemental Sulfur Formation: Implications to Hindered Chalcopyrite Dissolution.

Metal-deficient polysulfides have been argued for a long time to be responsible for the low kinetics of chalcopyrite leaching to extract copper. It has been shown that chalcopyrite surfaces are the source of sulfur that is oxidized to form polysulfides and elemental sulfur. Electronic structure calculations were performed for HxSnx-2 (x = 0, 1, 2 and n = 1...20), aiming to understand the effect of the pH on the growing chains and the formation of elemental sulfur. The estimated pKa1 of the H2Sn polysulfides converges from 4.2 (n = 3) to 3.4 (n ≥ 8), and the estimated pKa2 converges from 7.6 (n = 3) to 4.1 (n ≥ 8). The initial steps of the formation of polysulfide chains are more favored for protonated species. The elemental sulfur formation due to the decomposition of polysulfides to form smaller chains is mostly favored for protonated species with n smaller than 12. For larger chains, the decomposition is thermodynamically favored for polysulfides with any degree of protonation. The consequences of these results to the understanding of the mechanism of the chalcopyrite leaching process are discussed with the focus on the pH effect and the formation of elemental sulfur.

Peroxoniobium inhibits leukemia cell growth.

A new class of polyoxoniobate complex has been synthesized and characterized as a novel anticancer agent for photodynamic therapy. The complex inhibits the growth of chronic myelogenous leukemia cells with an IC50 value of 30 µM, in the dark. However, upon exposure to light (365 nm) there is a fivefold increase in the cytotoxic activity. Light radiation activate the complex with the formation of radical species capable of interacting with DNA according to our experimental and theoretical data.

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.

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).

Benzocaine complexation with p-sulfonic acid calix[n]arene: experimental ((1) H-NMR) and theoretical approaches.

The aim of this work was to study the interaction between the local anesthetic benzocaine and p-sulfonic acid calix[n]arenes using NMR and theoretical calculations and to assess the effects of complexation on cytotoxicity of benzocaine. The architectures of the complexes were proposed according to (1) H NMR data (Job plot, binding constants, and ROESY) indicating details on the insertion of benzocaine in the cavity of the calix[n]arenes. The proposed inclusion compounds were optimized using the PM3 semiempirical method, and the electronic plus nuclear repulsion energy contributions were performed at the DFT level using the PBE exchange/correlation functional and the 6-311G(d) basis set. The remarkable agreement between experimental and theoretical approaches adds support to their use in the structural characterization of the inclusion complexes. In vitro cytotoxic tests showed that complexation intensifies the intrinsic toxicity of benzocaine, possibly by increasing the water solubility of the anesthetic and favoring its partitioning inside of biomembranes.

Imogolite-like nanotubes: structure, stability, electronic and mechanical properties of the phosphorous and arsenic derivatives.

Imogolite is a single-walled aluminosilicate nanotube (NT) found in nature that can be easily synthesized, as well as its analogue aluminogermanate NT. Based on geometrical assumptions and pKa values, species such as H3PO4, H3PO3, H3AsO3, H3AsO4 could also be candidates to form imogolite-like structures. In the present work, we provide insights about the stability, electronic, structural and mechanical properties of possible imogolite like NTs by means of self-consistent charge density-functional tight-binding method (SCC-DFTB). Similarly to aluminogermanate, where the tetrahedral silicate groups are replaced by germanate, in this work tetrahedral silicate groups are substituted by phosphate, phosphite, arsenate and arsenite units in the imogolite structure. Detailed analysis is focused on structural properties, strain energy, band gap and Mulliken charges distribution. The calculated strain energy curves for all studied zigzag imogolite-like NTs present well-defined minima, which change as a consequence of composition variation. Moreover, the strain energy curves of armchair imogolite-like NTs also present minima, although in all cases less stable than zigzags by at least 2.2 meV per atom. The insulating NT behaviour changes after internal modification from silicate to phosphate, phosphite, arsenate and arsenite, as well as the charge distribution inside and outside the nanotubes.

Antioxidant activity of (+)-bergenin: a phytoconstituent isolated from the bark of Sacoglottis uchi Huber (Humireaceae).

(+)-Bergenin (1) was isolated from Sacoglottis uchi, a species of vegetable found in the Amazon region and popularly used for the treatment of several hepatic problems. The structure of 1 was fully characterized using IR, GC-MS and NMR (1D and 2D) analyses. This phytoconstituent has been used as an oriental folk medicine for the treatment of many diseases and shows antihepatotoxic properties. Tests with beta-carotene, DPPH and a heterogeneous Fenton system were carried out, confirming the antioxidant activity of 1. Theoretical calculations were performed to investigate the formation of the radical derivatives of 1 using *H, *OH, *CH(3), and *CCl(3) as initiator radicals. DFT thermodynamic calculations showed that the methoxyl group (O-6-CH(3)) is the most favorable site for radical attack. Frontier molecular orbital analysis showed that nucleophilic radical attack is favored on the aromatic ring of 1 where the LUMO is localized, with antibonding character with respect to the O-6-CH(3) bond. The possibilities of attack at other sites on 1 were investigated in detail in order to understand the regiospecificity of this reaction.

Study of angiotensin-(1-7) vasoactive peptide and its beta-cyclodextrin inclusion complexes: complete sequence-specific NMR assignments and structural studies.

We report the complete sequence-specific hydrogen NMR assignments of vasoactive peptide angiotensin-(1-7) (Ang-(1-7)). Assignments of the majority of the resonances were accomplished by COSY, TOCSY, and ROESY peak coordinates at 400MHz and 600MHz. Long-side-chain amino acid spin system identification was facilitated by long-range coherence transfer experiments (TOCSY). Problems with overlapped resonance signals were solved by analysis of heteronuclear 2D experiments (HSQC and HMBC). Nuclear Overhauser effects (NOE) results were used to probe peptide conformation. We show that the inclusion of the angiotensin-(1-7) tyrosine residue is favored in inclusion complexes with beta-cyclodextrin. QM/MM simulations at the DFTB/UFF level confirm the experimental NMR findings and provide detailed structural information on these compounds in aqueous solution.

Raman spectroscopy and DFT calculations of As(III) complexation with a cysteine-rich biomaterial.

Arsenite adsorption onto a protein-rich biomass and, more specifically, the chemical groups involved in the uptake were investigated using Raman spectroscopy and DFT calculations. The study was based on spectroscopic analyses of raw and arsenic-loaded biomass as well as standard samples of amino acids and arsenic salts. The predominant secondary structure of the protein was identified as the beta-sheet type, with some contribution from alpha-helix structures. The participation of sulphydryl groups from cystine/cysteine molecules during the adsorption of arsenite was demonstrated. Only the gauche-gauche-gauche (g-g-g) conformation type of the disulfide bonds was involved in arsenic complexation. The formation of a pyramidal trigonal As(HCys)(3) complex was modeled according to the density functional theory (DFT). The agreement of the DFT harmonic frequencies with the RAMAN spectra of the As(HCys)(3) complex demonstrated the relevant features of the cysteine-rich biomaterial regarding arsenic uptake as well as of the mechanism involved in the As(III)/biomass interaction at a molecular level. The results also illustrate that Raman spectroscopy can be successfully applied to investigate the mechanism of metal adsorption onto amorphous biomaterials.

Structure and dynamics of beta-cyclodextrin in aqueous solution at the density-functional tight binding level.

Structure and dynamics of beta-cyclodextrin (beta-CyD), a prototype host for inclusion compounds of biological interest, is investigated by means of density-functional based tight-binding molecular dynamics (MD) simulations. The computational protocol is benchmarked against available experimental data and first-principles calculations. Solvent-solute interactions, including the diffusion into and dwell time of the solvent in the cavity of beta-CyD, are studied with a hybrid QM/MM method. Comparison of MD simulations of beta-CyD in the gas phase and in water shows that the solvent reduces the flexibility of the structure framework, while the terminal hydroxyl groups become more flexible and are embedded in a network of hydrogen bonds. Our 160 ps MD simulations, provide enough sampling to discuss the dynamics of the water inside the cavity. The dwell time of the encapsulated water molecule has a wide distribution with a peak at 70 fs. Surprisingly, despite only the 17% difference between the "top" and "bottom" opening area of the beta-CyD cone, 64% of the water molecules enter the cavity through the slightly bigger "bottom" aperture.

Imogolite nanotubes: stability, electronic, and mechanical properties.

The aluminosilicate mineral imogolite is composed of single-walled nanotubes with stoichiometry of (HO)(3)Al(2)O(3)SiOH and occurs naturally in soils of volcanic origin. In the present work we study the stability and the electronic and mechanical properties of zigzag and armchair imogolite nanotubes using the density-functional tight-binding method. The (12,0) imogolite tube has the highest stability of all tubes studied here. Uniquely for nanotubes, imogolite has a minimum in the strain energy for the optimum structure. This is in agreement with experimental data, as shown by comparison with the simulated X-ray diffraction spectrum. An analysis of the electronic densities of states shows that all imogolite tubes, independent on their chirality and size, are insulators.

Monte Carlo simulation of cisplatin molecule in aqueous solution.

The Lennard-Jones (12-6) parameters were obtained for all atoms of cisplatin molecule using the ab initio quantum mechanical potential energy surface for the water-cisplatin interaction as reference data. The parameters found were (epsilon/kcal.mol(-1) and sigma/angstroms) 1.0550, 3.6590 (Pt); 0.0381, 4.6272 (Cl); 0.0455, 3.3783 (N); and 0.0185, 0.0936 (H) and provided very good results for the description of the aqueous solution of cisplatin through Monte Carlo simulation. From statistical analysis of solute-solvent interactions, we observed that the NH3 groups are involved in 53% of the calculated hydrogen bonds with a significant contribution from chlorides (41%) and only 6% involving the Pt center. This is in agreement with the expected behavior for such molecules. Two hydration shells with 22 and 81 water molecules, respectively, centered around 4.6 and 7.3 angstroms were found from the center of mass pair correlation function analysis. The cisplatin atomic Lennard-Jones parameters are reported for the first time, and they might be useful for studying the structure, properties, and processes of cisplatin-like molecules in aqueous solution, including explicitly the solvent effect.

An Efficient a Posteriori Treatment for Dispersion Interaction in Density-Functional-Based Tight Binding.

The performance of density functional theory (DFT) (VWN-LDA, PBE-GGA, and B3LYP hybrid functionals), density-functional-based tight binding (DFTB), and ab initio methods [HF, MP2, CCSD, and CCSD(T)] for the treatment of London dispersion is investigated. Although highly correlated ab initio methods are capable of describing this phenomenon, if they are used with rather large basis sets, DFT methods are found to be inadequate for the description of H2/PAH (polycyclic aromatic hydrocarbon) interactions. As an alternative approach, an a posteriori addition of a van der Waals term to DFTB is proposed. This method provides results for H2/PAH interactions in close agreement with MP2 and higher-level ab initio methods. Bulk properties of graphite also compare well with the experimental data.

Potentiometric, spectrophotometric and density functional study of the interaction of N-hydroxyacetamide with oxovanadium(IV): the influence of ligand to the V(IV)/V(V) oxi-reduction reaction.

The interaction of N-hydroxyacetamide (acetohydroxamic acid, HL) with V(IV) in aqueous solution has been investigated using potentiometric and spectrophotometric experiments. Density functional method (DFT) has been used aiming to understand the ligand chelation at a molecular level. Stability constants have been estimated for species with the metal/ligand ratios 1:1 and 1:2 from spectrophotometric and potentiometric measurements. The stability of these V(IV) species toward oxidation has been investigated. Experiments carried out in an oxygen atmosphere led to the displacement of the titration curves with respect to the one obtained under inert atmosphere. Spectrophotometric evidence of the V(IV)/V(V) oxidation in the presence of N-hydroxyacetamide is presented. It has been shown that V(IV)/V(V) oxidation in the presence of N-hydroxyacetamide by the oxygen can be simulated using the standard programs for simulating the equilibrium in a multiligand/multimetal system. In this approach, the oxygen is considered a ligand and the log beta estimated from the standard oxidation potential. The structure and respective tautomers of the species have been optimized from DFT calculations. Geometrical and thermodynamical properties have been estimated for the most stable complexes. The VOL-->VOL(2) equilibrium constant has been theoretically estimated with a less than 1.5 logarithmic unit of error with respect to the experimental estimate. The oxidation process has also been investigated and it is adequately described by the equation: 4[VOL(2)]+2H(2)O+O(2)-->4[VO(OH)L(2)]. The calculated value of DeltaG for this reaction is about -46.2 kcal mol(-1), in excellent agreement with the experimental estimates.