Antonio M. J. C. Neto

The basic antioxidant structure for flavonoid derivatives.

AbstractAn antioxidant structure–activity study is carried out in this work with ten flavonoid compounds using quantum chemistry calculations with the functional of density theory method. According to the geometry obtained by using the B3LYP/6-31G(d) method, the HOMO, ionization potential, stabilization energies, and spin density distribution showed that the flavonol is the more antioxidant nucleus. The spin density contribution is determinant for the stability of the free radical. The number of resonance structures is related to the π-type electron system. 3-hydroxyflavone is the basic antioxidant structure for the simplified flavonoids studied here. The electron abstraction is more favored in the molecules where ether group and 3-hydroxyl are present, nonetheless 2,3-double bond and carbonyl moiety are facultative. FigureThe basic antioxidant structure for flavonoid derivatives

A combined experimental and theoretical approach for radical-scavenging activity of edaravone and its related derivatives

The experimental and theoretical study for evaluation of scavenging activity of edaravone (S1) and related derivatives, such as antipyrine (S2), dipyrone (S3), and phenylbutazone (S4), was carried out against DPPH and ABTS radicals. Structure–activity relationship study was performed using quantum chemical calculations at the DFT/B3LYP level of theory along with the 6-31G* basis sets. S1 and S4 are more effective scavengers against DPPH and ABTS. We observed little effects of S2 and S3 at several concentrations against these two free radicals. The calculations of HOMO, ionization potential, and bond dissociation energy confirmed that a hydrogen transfer is more preferential than an electron transfer. The radical stability of these compounds is related with spin densities. In accordance with experimental and theoretical results, edaravone is more active than phenylbutazone as scavenging drug.

Single-molecular diodes based on opioid derivatives

We propose an efficient single-molecule rectifier based on a derivative of opioid. Electron transport properties are investigated within the non-equilibrium Green’s function formalism combined with density functional theory. The analysis of the current–voltage characteristics indicates obvious diode-like behavior. While heroin presents rectification coefficient R>1, indicating preferential electronic current from electron-donating to electron-withdrawing, 3 and 6-acetylmorphine and morphine exhibit contrary behavior, R<1. Our calculations indicate that the simple inclusion of acetyl groups modulate a range of devices, which varies from simple rectifying to resonant-tunneling diodes. In particular, the rectification rations for heroin diodes show microampere electron current with a maximum of rectification (R=9.1) at very low bias voltage of ∼0.6 V and (R=14.3)∼1.8 V with resistance varying between 0.4 and 1.5 M Ω. Once most of the current single-molecule diodes usually rectifies in nanoampere, are not stable over 1.0 V and present electrical resistance around 10 M. Molecular devices based on opioid derivatives are promising in molecular electronics.

Involvement of electron and hydrogen transfers through redox metabolism on activity and toxicity of the nimesulide

AbstractAn electronic study of nimesulide was performed by using density functional theory calculations. The activities of the six different derivatives were related with electron donating or accepting capacities. All compounds which had nitro moiety had low electron donating and high electron accepting capacities. However, the reduced derivative of nimesulide have more electron donating capacity than other compounds. The highest spin density contribution in nitro and lowest spin density contribution on phenoxyl moieties can be related with preferential metabolism by reduction when compared with the oxidation. The redox behavior between nitro and amino groups can be related with anti-inflammatory mechanism of nimesulide. These results explain the redox influence of nitro moiety on biological metabolism and mechanism of nimesulide. Graphical AbstractElectron and hydrogen transfers on redox metabolism of nimesulide

Thermodynamic DFT analysis of natural gas

AbstractDensity functional theory was performed for thermodynamic predictions on natural gas, whose B3LYP/6–311++G(d,p), B3LYP/6–31+G(d), CBS-QB3, G3, and G4 methods were applied. Additionally, we carried out thermodynamic predictions using G3/G4 averaged. The calculations were performed for each major component of seven kinds of natural gas and to their respective air + natural gas mixtures at a thermal equilibrium between room temperature and the initial temperature of a combustion chamber during the injection stage. The following thermodynamic properties were obtained: internal energy, enthalpy, Gibbs free energy and entropy, which enabled us to investigate the thermal resistance of fuels. Also, we estimated an important parameter, namely, the specific heat ratio of each natural gas; this allowed us to compare the results with the empirical functions of these parameters, where the B3LYP/6–311++G(d,p) and G3/G4 methods showed better agreements. In addition, relevant information on the thermal and mechanic resistance of natural gases were investigated, as well as the standard thermodynamic properties for the combustion of natural gas. Thus, we show that density functional theory can be useful for predicting the thermodynamic properties of natural gas, enabling the production of more efficient compositions for the investigated fuels. Graphical abstractInvestigation of the thermodynamic properties of natural gas through the canonical ensemble model and the density functional theory

Understanding the cytotoxicity or cytoprotective effects of biological and synthetic quinone derivatives by redox mechanism.

AbstractQuinones represent an important class of biological compounds, but are also involved with toxicological intermediates and among their hazardous effects include cytotoxicity, immunotoxicity, and carcinogenesis. The structure–toxicity relationship for quinone derivatives has been used to cytotoxicity or cytoprotective effects by redox mechanism is determined using quantum chemical calculations through the density functional theory (DFT). According to our DFT study, the electron acceptance is related with LUMO, electron affinity, and stabilization energy values. The highest spin density distribution in the heteroatoms is more favored for the more cytotoxic compounds. The electrophilic capacities of these compounds have been related with LUMO values. The cytotoxic properties of quinones are related to the stabilization energy after electron accepting by redox mechanism. Electron affinity is the most relevant parameter related to toxicity mechanism. Regioisomers has different electrophilic capacity. The electrophilicity increases on molecules containing electron-withdrawing groups (EWG) and reduces on molecules containing electron-donating groups (EDG). These results explain the toxic difference between natural and synthetic quinone derivatives and can be used in the design and study of new drugs. Graphical AbstractBiological and synthetic ortho and para quinone derivatives

Sugar moiety has a synergistic effect on hydroxylated xanthone for better antioxidant activity of mangiferin

The structure–antioxidant relationship of mangiferin was elucidated by means of quantum chemistry calculations. The density functional theory level of theory was used for antioxidant pharmacophore selection. According to the obtained geometry by using the DFT/B3LYP/6-31+G(d,p) values, HOMO, ionization potential, bond dissociation energy, stabilization energy, and spin density distribution, the catechol moiety is more important for the antioxidant capacity than the resorcinol moiety. However, the sugar is a strong electron-withdrawing group due to its hydrogen bond formation with the resorcinol moiety of xanthone ring. The hydrogen transfer is more important for the antioxidant activity than the electron transfer. The hydrogen abstractions in the ortho positions are more favored than the meta positions. Thus, our results show a synergistic effect between xanthone and sugar rings.

Time-Dependent Density Functional Theory Analysis of Triphenylamine-Functionalized Graphene Doped with Transition Metals for Photocatalytic Hydrogen Production

The electronic structures and optical properties of triphenylamine-functionalized graphene (G-TPA) doped with transition metals, using water as a solvent, were theoretically investigated to verify the efficiency of photocatalytic hydrogen production with the use of transition metals. This study was performed by Density Functional Theory and Time-dependent Density Functional Theory through Gaussian 09W software, adopting the B3LYP functional for all structures. The 6-31g(d) basis set was used for H, C and N atoms, and the LANL2DZ basis set for transition metals using the Effective Core Potentials method. Two approaches were adopted: (1) using single metallic dopants (Ni, Pd, Fe, Os and Pt) and (2) using combinations of Ni with the other dopants (NiPd, NiPt, NiFe and NiOs). The DOS spectra reveal an increase of accessible states in the valence shell, in addition to a gap decrease for all dopants. This doping also increases the absorption in the visible region of solar radiation where sunlight is most intense (400 nm to 700 nm), with additional absorption peaks. The results lead us to propose the G-TPA structures doped with Ni, Pd, Pt, NiPt or NiPd to be novel catalysts for the conversion of solar energy for photocatalytic hydrogen production, since they improve the absorption of solar energy in the range of interest for solar radiation; and act as reaction centers, reducing the required overpotential for hydrogen production from water.

Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13

In this work, the binding mechanism of new Polyketide Synthase 13 (Pks13) inhibitors has been studied through molecular dynamics simulation and free energy calculations. The drug Tam1 and its analogs, belonging to the benzofuran class, were submitted to 100 ns simulations, and according to the results obtained for root mean square deviation, all the simulations converged from approximately 30 ns. For the analysis of backbone flotation, the root mean square fluctuations were plotted for the Cα atoms; analysis revealed that the greatest fluctuation occurred in the residues that are part of the protein lid domain. The binding free energy value (ΔGbind) obtained for the Tam16 lead molecule was of −51.43 kcal/mol. When comparing this result with the ΔGbind values for the remaining analogs, the drug Tam16 was found to be the highest ranked: this result is in agreement with the experimental results obtained by Aggarwal and collaborators, where it was verified that the IC50 for Tam16 is the smallest necessary to inhibit the Pks13 (IC50 = 0.19 μM). The energy decomposition analysis suggested that the residues which most interact with inhibitors are: Ser1636, Tyr1637, Asn1640, Ala1667, Phe1670, and Tyr1674, from which the greatest energy contribution to Phe1670 was particularly notable. For the lead molecule Tam16, a hydrogen bond with the hydroxyl of the phenol not observed in the other analogs induced a more stable molecular structure. Aggarwal and colleagues reported this hydrogen bonding as being responsible for the stability of the molecule, optimizing its physic-chemical, toxicological, and pharmacokinetic properties.

Intermolecular interactions between DNA and Methamphetamine, Amphetamine, Ecstasy and their major metabolites.

In this work, we carried out a theoretical investigation regarding amphetamine-type stimulants, which can cause central nervous system degeneration, interacting with human DNA. These include amphetamine, methamphetamine, 3,4-Methylenedioxymethamphetamine (also known as ecstasy), as well as their main metabolites. The studies were performed through molecular docking and molecular dynamics simulations, where molecular interactions of the receptor–ligand systems, along with their physical–chemical energies, were reported. Our results show that 3,4-Methylenedioxymethamphetamine and 3,4-Dihydroxymethamphetamine (ecstasy) present considerable reactivity with the receptor (DNA), suggesting that these molecules may cause damage due to human-DNA. These results were indicated by free Gibbs change of bind (ΔGbind) values referring to intermolecular interactions between the drugs and the minor grooves of DNA, which were predominant for all simulations. In addition, it was observed that 3,4-Dihydroxymethamphetamine (ΔGbind = −13.15 kcal/mol) presented greater spontaneity in establishing interactions with DNA in comparison to 3,4-Methylenedioxymethamphetamine (ΔGbind = −8.61 kcal/mol). Thus, according with the calculations performed our results suggest that the 3,4-Methylenedioxymethamphetamine and 3,4-Dihydroxymethamphetamine have greater probability to provide damage to human DNA fragments.