Marcus V. J. Rocha

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.

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.

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.

Orbital signatures as a descriptor of regioselectivity and chemical reactivity: the role of the frontier orbitals on 1,3-dipolar cycloadditions.

The FERMO concept emerges as a powerful and innovative implement to investigate the role of molecular orbitals applied to the description of breakage and formation of chemical bonds. In this work, Hartree-Fock (HF) theory and density functional (DFT) calculations were performed for a series of four reactions of 1,3-dipolar cycloadditions and were analyzed by molecular orbital (MO) energies, charge transfer, and molecular dynamics (ADMP) techniques for direct dynamics using the DFT method. The regioselectivity for a series of four 1,3-dipolar cycloaddition reactions was studied here using global and local reactivity indexes. We observed that the HOMO energies are insufficient to describe the behavior of these reactions when there is the presence of heteroatoms. By using the frontier effective-for-reaction molecular orbital (FERMO) concept, the reactions that are driven by HOMO, and those that are not, can be better explained, independent of the calculation method used, because both HF and Kohn-Sham methodologies lead to the same FERMO.

Ionic desorption in PMMA-gamma-Fe2O3 hybrid materials induced by fast electrons: an experimental and theoretical investigation.

Poly(methylmetacrilate)-maghemite (PMMA-gamma-Fe2O3) hybrid material was studied by the electron stimulated ion desorption (ESID) techniques coupled with time-of-flight mass spectrometry (TOF-MS) and theoretical investigation about its fragmentation. Moreover, atomic force microscopy was utilized to characterize the morphology before and after ionic desorption. ESID results indicated differences of pattern fragmentation for different compositions of hybrid material in comparison with neat PMMA. Theoretical studies suggest that kinetics effects can take place in the fragmentation process and electrostatic contributions were important in the stabilization of PMMA on maghemite after the grafting process.

Construction and assessment of reaction models between F1F0-synthase and organotin compounds: molecular docking and quantum calculations

Organotin compounds are the active components of some fungicides, which are potential inhibitors of the F1F0-ATP synthase. The studies about the reaction mechanism might indicate a pathway to understand how these compounds work in biological systems, however, has not been clarified so far. In this line, molecular modeling studies and density functional theory calculations were performed in order to understand the molecular behavior of those compounds when they interact with the active site of the enzyme. Our findings indicate that a strong interaction with His132 can favor a chemical reaction with organotin compounds due to π–π stacking interactions with aromatic rings of organotin compounds. Furthermore, dependence on molecule size is related to possibility of reaction with the amino acid residue His132. Thus, it can also be noticed, for organotin compounds, that substituents with four carbons work by blocking the subunit a, in view of the high energy transition found characterized by steric hindrance.

Degradation of organic compounds in a fenton system based on chitosan/Fe0/Fe2O3 composites: a theoretical and experimental study

Chitosan is a polymer with interesting characteristics for use in catalysis, such as biocompatibility, high chemical reactivity and stability under various conditions. Seeking new applications, a new hybrid material was synthesized for use in the degradation of organic compound. A synthesis route proposed led to the formation of a material in the form of film. The characterization data indicated the presence of hematite, as well as metallic iron. In addition, a theoretical model for interaction of iron with chitosan was proposed. Molecular dynamics simulations indicate that non-Coulomb interactions modulate the adsorption process between reactive red dye and chitosan. The catalytic behavior of these hybrid materials was investigated for the H2O2 decomposition to O2 and the degradation of reactive red dye. The hybrid material showed high degradation capacity, confirming this material as an efficient heterogeneous Fenton catalysts.

Structure and bonding in NbX5 X = (F, Cl, Br and I) complexes: a molecular orbital perspective in the C–H bond activation

In the present work, theoretical studies of the reactivity and stability of the NbX5 complexes (X = F, Cl, Br and I) were carried out in the methane C–H bond activation. To study the chemical bonds formation of these complexes, an energy decomposition analysis was performed together with QTAIM calculations. The main results indicated that the interaction and binding energies are higher for NbF5 in relation to the halogen series. The niobium complexes gaps are influenced by the electronegativity of the halogens and the Nb–X bonding lengths. According to the energy diagram, the electrons less connected to the bond are σNb–I; on the other hand, the best electron acceptor is σ*Nb–F. The QTAIM calculations confirmed stronger Nb–X chemical bonds in NbF5 complexes. Regarding the reactivity of the niobium complexes, the overall results indicate better thermodynamic and kinetic conditions for the NbF5 complex.