Teodorico C. Ramalho

Photocatalytic degradation of methylene blue by TiO2–Cu thin films: Theoretical and experimental study

In this work the effect of doping concentration and depth profile of Cu atoms on the photocatalytic and surface properties of TiO(2) films were studied. TiO(2) films of about 200 nm thickness were deposited on glass substrates on which a thin Cu layer (5 nm) was deposited. The films were annealed during 1s to 100°C and 400°C, followed by chemical etching of the Cu film. The grazing incidence X-ray fluorescence measurements showed a thermal induced migration of Cu atoms to depths between 7 and 31 nm. The X-ray photoelectron spectroscopy analysis detected the presence of TiO(2), Cu(2)O and Cu(0) phases and an increasing Cu content with the annealing temperature. The change of the surface properties was monitored by the increasing red-shift and absorption of the ultraviolet-visible spectra. Contact angle measurements revealed the formation of a highly hydrophilic surface for the film having a medium Cu concentration. For this sample photocatalytic assays, performed by methylene blue discoloration, show the highest activity. The proposed mechanism of the catalytic effect, taking place on Ti/Cu sites, is supported by results obtained by theoretical calculations.

Molecular modeling of Mycobacterium tuberculosis DNA gyrase and its molecular docking study with gatifloxacin inhibitors.

Abstract Mycobacterium tuberculosis (Mt) is a leading cause of infectious disease in the world today. This outlook is aggravated by a growing number of Mt infections in individuals who are immunocompromised as a result of HIV infections. Thus, new and more potent anti-tuberculosis agents are necessary. Therefore, DNA gyrase was selected as a target enzyme to combat Mt. In this work, the first three-dimensional molecular model of the hypothetical structures for the Mycobacterium tuberculosis DNA gyrase (mtDNAg) was elucidated by a homology modeling method. In addition, the orientations and binding affinities of some gatifloxacin analogs with those new structures were investigated. Our findings could be helpful for the design of new more potent gatifloxacin analogs.

Construction and Assessment of Reaction Models of Class I EPSP Synthase: Molecular Docking and Density Functional Theoretical Calculations

Abstract The high frequency of contamination by herbicides suggests the need for more active and selective herbicides. Glyphosate is the active component of one of the top-selling herbicides, which is also a potent EPSP synthase inhibitor. That is a key enzyme in the shikimic acid pathway, which is found only in plants and some microorganisms. Thus, EPSP synthase is regarded as a prime target for herbicides. In this line, molecular modeling studies using molecular dynamics simulations and DFT techniques were performed to understand the interaction of glyphosate and its analogs with the wild type enzyme and Gly96Ala mutant EPSP synthase. In addition, we investigated the reaction mechanism of the natural substrate. Our findings indicate some key points to the design of new selective glyphosate derivates.

Homology modeling of wild-type, D516V, and H526L Mycobacterium tuberculosis RNA polymerase and their molecular docking study with inhibitors.

Abstract Rifamicyns (Rifs) are antibiotic widely used for the treatment of tuberculosis (TB); nevertheless, their efficacy has been limited by a high percentage of mutations, principally in the rpoB gene. In this work, the first three-dimensional molecular model of the hypothetical structures for the wild-type and D516V and H526L mutants of Mycobacterium tuberculosis (mtRNAP) were elucidated by a homology modeling method. In addition, the orientations and binding affinities of some Rifs with those new structures were investigated. Our findings could be helpful for the design of new more potent rifamycin analogs.

Nanostructured δ-FeOOH: a novel photocatalyst for water splitting

We report on the first use of nanostructured δ-FeOOH as a promising photocatalyst for hydrogen production. The high surface area, interparticle mesoporosity, small particle size and band gap energy in the visible region make nanostructured δ-FeOOH a suitable candidate for use as a photocatalyst.

Binding Mode Analysis of 2,4-diamino-5-methyl-5-deaza-6-substituted Pteridines with Mycobacterium tuberculosis and Human Dihydrofolate Reductases

Abstract There are major differences between the structures of human dihydrofolate reductase (hD-HFR) and Mycobacterium tuberculosis dihydrofolate reductase (mtDHFR). These differences may allow the design of more selective mtDHFR inhibitors. In this paper, we have used docking approaches to study the binding orientations and predict binding affinities of 2,4-diamino-5-methyl-5-deazapteridines derivatives in both hDHFR and mtDHFR. Our results of molecular docking combined with experimental data for inhibition of the human and mycobacterial dihydrofolate reductases suggest the presence of empty spaces around the 2,4-diaminodeazapteridine and N10-phenyl rings in the mtDHFR active site that are not found in the hDHFR-bound structures. Preparation of new analogs with substituents attached to C7 of the pteridine nucleus and positions 3 and 4 of the N10-phenyl group should increase the affinity and selectivity for mtDHFR.

Solvent effects on 13C and 15N shielding tensors of nitroimidazoles in the condensed phase: a sequential molecular dynamics/quantum mechanics study

Na nd 13 CN MR chemical shifts for three nitroimidazoles have been calculated and compared with experimental data. The solvent effects on NMR spectra were simulated with the polarizable continuum model (PCM) and an alternative sequential molecular dynamics/quantum mechanics methodology (S-MD/QM). The sampling of the structures for the quantum mechanical calculations is made by using the interval of statistical correlation obtained from the autocorrelation function of the energy. Magnetic shielding tensors were evaluated .

Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View

Emissions of greenhouse gases due to human activities have been well documented as well as the effects on global warming resulting from it. Efforts to reduce greenhouse gases at the source are crucial to curb climate change, but due to insignificant economic incentives to reduce usage of fossil fuels, not a lot of progress has been made by this route. This necessitates additional measures to reduce the occurrence of greenhouse gases in the atmosphere. Here we used theoretical methods to study the solubility of carbon dioxide in ionic liquids (ILs) since sequestration of CO2 in ILs has been proposed as a possible technology for reducing the emissions of CO2 to the atmosphere. Ionic liquids form a class of solvents with melting temperatures below 100 °C and, due to very low vapor pressures, which are not volatile. We have performed molecular dynamics (MD) simulations of 1-ethyl-3-methylimidazolium (C2mim) bis(trifluoromethylsulfonyl)imide (Tf2N) and its mixtures with carbon dioxide in order to investigate the CO2 concentration effect on the CO2-cation and CO2-anion interactions. A systematic investigation of CO2 concentration effects on resulting equilibrium liquid structure, and the local environment of the ions is provided. The Quantum Theory of Atoms in Molecules (QTAIM) was used to determine the interaction energy for CO2-cation and CO2-anion complexes from uncorrelated structures derived from MD simulations. A spatial distribution function analysis demonstrates the specific interactions between CO2 and the ionic liquid. Our findings indicate that the total volume of the system increases with the CO2 concentration, with a molar volume of CO2 of about 0.038 L/mol, corresponding to liquid CO2 under a pressure of 100 bar. In other words, the IL effectively pressurizes the CO2 inside its matrix. The thermodynamics of CO2 solvation in C2 min-Tf2N were computed using free energy techniques, and the solubility of CO2 is found to be higher in this IL (-3.7 ± 1 kcal/mol) than in water (+0.2 kJ/mol), predominantly due to anion-CO2 interactions.

Thermal and solvent effects on the NMR and UV parameters of some bioreductive drugs.

15N NMR chemical shifts and n-->pi* electronic transition energy for metronidazole (1) has been calculated and compared with experimental data. A detailed computational study of 1 is presented, with special attention to the performance of various theoretical methods for reproducing spectroscopic parameters in solution. The most sophisticated approach involves density functional based on the Car-Parrinello molecular dynamics simulations of 1 in aqueous solution (BP86 level) and averaging chemical shifts and deltaE(n-->pi*) over snapshots from the trajectory. In the NMR and UV calculations for these snapshots (performed at the B3LYP level), a small number of discrete water molecules are retained, and the remaining bulk solution effects are included via a polarizable continuum model (PCM). A good agreement with experiment is also obtained using static geometry optimization and NMR computation of pristine 1 employing a PCM approach. Further theoretical predictions are also reported for 17O NMR and deltaE(n-->pi*) of three hydroxycinnamic acid derivatives, which suggest that it is essential to incorporate the dynamics and solvent effects for NMR and UV calculations in the condensed phase.

Understanding the Molecular Behavior of Organotin Compounds to Design their Effective Use as Agrochemicals: Exploration via Quantum Chemistry and Experiments

Abstract The high frequency of contamination by herbicides suggests the need for more active and selective agrochemicals. Organotin compounds are the active component of some herbicides, such as Du-Ter and Brestan, which is also a potent inhibitor of the F1Fo ATP Synthase. That is a key enzyme, because the ATP production is one of the major chemical reactions in living organisms. Thus ATP Synthase is regarded as a prime target for organotin compounds. In this line, molecular modeling studies and DFT calculations were performed in order to understand the molecular behavior of those compounds in solution. In addition, we investigated the reaction mechanism by ESI-MS analyses of the diphenyltin dichloride. Our findings indicate that an unstable key-intermediate generated in situ might take place in the reaction with ATP Synthase.