On the Role of the Carboxyl Group to the Protective Effect of o-Dihydroxybenzoic Acids to Saccharomyces cerevisiae Cells upon Induced Oxidative Stress

In the present work, the role of the carboxyl group of o-dihydroxybenzoic acids (pyrocatechuic, 2,3-diOH-BA and protocatechuic, 3,4-diOH-BA) on the protection against induced oxidative stress in Saccharomyces cerevisiae was examined. Catechol (3,4-diOH-B) was included for comparison. Cell survival, antioxidant enzyme activities, and TBARS level were used to evaluate the efficiency upon the stress induced by H2O2 or cumene hydroperoxide. Theoretical calculation of atomic charge values, dipole moment, and a set of indices relevant to the redox properties of the compounds was also carried out in the liquid phase (water). Irrespective of the oxidant used, 2,3-diOH-BA required by far the lowest concentration (3–5 μM) to facilitate cell survival. The two acids did not activate catalase but reduced superoxide dismutase activity (3,4-diOH-BA>2,3-diOH-BA). TBARS assay showed an antioxidant effect only when H2O2 was used; equal activity for the two acids and inferior to that of 3,4-diOH B. Overall, theoretical and experimental findings suggest that the 2,3-diOH-BA high activity should be governed by metal chelation. In the case of 3,4-diOH BA, radical scavenging increases, and chelation capacity decreases. The lack of carboxyl moiety (3,4-diOH B) adds to radical scavenging, interaction with lipophilic free radicals, and antioxidant enzymes. The present study adds to our knowledge of the antioxidant mechanism of dietary phenols in biological systems.

A Bond Bundle Case Study of Diels-Alder Catalysis Using Oriented Electric Fields

Bond bundles are chemical bonding regions, analogous to Bader atoms, uniquely defined according to the topology of the gradient bundle condensed charge density, itself obtained by a process of infinitesimal partitioning of the three-dimensional charge density into differential zero-flux surface bounded regions. Here we use bond bundle analysis to investigate the response of the charge density to an oriented electric field in general, and the catalytic effect of such a field on Diels-Alder reactions in particular, which in this case is found to catalyze by allowing the transition state valance bond bundle configuration to be achieved earlier along the reaction pathway. Using precise numerical values, we arrive at the conclusion that chemical reactions and electric field catalysis can be understood in terms of intra-atomic charge density redistribution, i.e., that charge shifts within more so than between atoms account for the making and breaking of bonds.

Using Atomic Charges to Model Molecular Polarization.

We review different models for introducing electrical polarization in force fields, with special focus on methods where polarization is modelled at the atomic charge level. While electric polarization has been...

Semiempirical Quantum Chemical and Ab Intio Study of Co(Ii), Ni(Ii),Cu(Ii) and Zn(Ii) Complexes with the Azo Dye Derived from 4-Amino Antipyrine and 2,4-Dihydroxy Acetopheone

Semi-empirical quantum chemical calculation was made to study the nucleophilicity of the ligand and to study the mode of bonding between the ligand and the metal ions. The natural atomic charge at different atomic sites of the ligand has been calculated along with the electrostatic potential map to predict the reactive sites for electrophilic and nucleophilic attack. The theoretical spectral data such as IR, NMR and electronic have been calculated and compared with the experimentally generated data.

Investigative properties of CeO2 doped with niobium: A combined characterization and DFT studies

Catalytic capacity of ceria mainly stems from a facile switch in the Ce oxidation states from +4 to +4 − x. While various experimental and computational studies pinpoint the reduction chemistry of Ce atom through the creation of oxygen vacancies, the analogous process when ceria surface is decorated with cations remains poorly understood. Where such results are available, a synergy between experimental and first principle calculation is scarce. Niobium materials are evolving and their use in catalysis is being widely investigated due to their high surface acidity and thermal and chemical stability. This study aims to report structural and electronic properties of various configurations of mixed Ce–Nb oxides and elaborates on factors that underpin potential catalytic improvements. Evaluations of the samples through X-ray diffraction (XRD), Fourier transform infrared (FTIR), N2-adsorption–desorption, scanning electron microscope (SEM), energy dispersive spectroscope (EDS), and thermogravimetric (TGA) analyses are examined and discussed. First principles density functional theory (DFT) calculations provide structural features of the Ce–Nb solutions at low concentration of Nb via computing atomic charge distribution. Contraction in the lattice parameter after Nb doping was confirmed with both XRD and DFT results. SEM analysis reveals particle growth at the loading of 50 wt%. FTIR results established the Ce–Nb–O bond at 1,100 cm−1 and the TGA analysis confirms the thermal stability of Nb-doped ceria. Tetrahedral O atoms demonstrate an increase in electronegativity and this in turn facilitates catalytic propensity of the material because the O atoms will exhibit higher affinity for adsorbed reactants. Cerium oxide (CeO2) after Nb doping displays a noticeable band gap narrowing, confirming the possible improvement in the catalytic behavior. The 4d states of the Niobium pentoxide (Nb2O5) is found to fill up the 4f states of CeO2 around the Fermi energy level promoting electrons excitation in the CeO2. Reported electronic, structural, and thermal characteristics herein indicate promising catalytic applications of niobium-promoted ceria.

A Bond Bundle Case Study of Diels-Alder Catalysis Using Oriented Electric Fields

Bond bundles are chemical bonding regions, analogous to Bader atoms, uniquely defined according to the topology of the gradient bundle condensed charge density, itself obtained by a process of infinitesimal partitioning of the three-dimensional charge density into differential zero-flux surface bounded regions. Here we use bond bundle analysis to investigate the response of the charge density to an oriented electric field in general, and the catalytic effect of such a field on Diels-Alder reactions in particular, which in this case is found to catalyze by allowing the transition state valance bond bundle configuration to be achieved earlier along the reaction pathway. Using precise numerical values, we arrive at the conclusion that chemical reactions and electric field catalysis can be understood in terms of intra-atomic charge density redistribution, i.e., that charge shifts within more so than between atoms account for the making and breaking of bonds.

DFT-D4 Insight into the Inclusion of Amphetamine and Methamphetamine in Cucurbit[7]uril: Energetic, Structural and Biosensing Properties

The host–guest interactions of cucurbit[7]uril (CB[7]) as host and amphetamine (AMP), methamphetamine (MET) and their enantiomeric forms (S-form and R-form) as guests were computationally investigated using density functional theory calculations with the recent D4 atomic-charge dependent dispersion corrections. The analysis of energetic, structural and electronic properties with the aid of frontier molecular orbital analysis, charge decomposition analysis (CDA), extended charge decomposition analysis (ECDA) and independent gradient model (IGM) approach allowed to characterize the host–guest interactions in the studied systems. Energetic results indicate the formation of stable non-covalent complexes where R-AMP@CB[7] and S-AMP@CB[7] are more stable thermodynamically than R-MET@CB[7] and S-MET@CB[7] in gas phase while the reverse is true in water solvent. Based on structural analysis, a recognition mechanism is proposed, which suggests that the synergistic effect of van der Waals forces, ion–dipole interactions, intermolecular charge transfer interactions and intermolecular hydrogen bonding is responsible for the stabilization of the complexes. The geometries of the complexes obtained theoretically are in good agreement with the X-ray experimental structures and indicate that the phenyl ring of amphetamine and methamphetamine is deeply buried into the cavity of CB[7] through hydrophobic interactions while the ammonium group remains outside the cavity to establish hydrogen bonds with the portal oxygen atoms of CB[7].

Indirect electrochemical degradation of acetaminophen: process performance, pollutant transformation, and matrix effects evaluation

Acetaminophen (ACE), a highly consumed pharmaceutical, was degraded in aqueous matrices by reactive chlorine species (RCS) electrogenerated using Ti/IrO2 electrodes. Although this pollutant has been extensively treated by electrochemical techniques, little information is known about its degradation in fresh urine by electrogenerated RCS, and the understanding of its transformations using analyses of atomic charge. In this work, these two topics were discussed. Initially, the effect of current (10-40 mA) and supporting electrolyte (considering typical ions present in surface water and urine (Cl- and SO42-)) on the electrochemical system was evaluated. Then, the kinetics and primary transformations products involved in the elimination of ACE were described. It was found that, in distilled water, the process at 40 mA in NaCl presence led to 100 % of ACE degradation (10 min, 0.056 Ah L-1). Theoretical analyses of atomic charge for ACE indicated that the amide group is the most susceptible to attacks by RCS such as HOCl. On the other hand, degradation of acetaminophen in synthetic fresh urine was slower (21% of degradation after 60 min of treatment) than in distilled water. This was attributed to the other substances in the urine matrix, which induce competition for the degrading RCS.

Improvement of the Force Field for β-d-Glucose with Machine Learning

While the construction of a dependable force field for performing classical molecular dynamics (MD) simulation is crucial for elucidating the structure and function of biomolecular systems, the attempts to do this for glycans are relatively sparse compared to those for proteins and nucleic acids. Currently, the use of GLYCAM06 force field is the most popular, but there have been a number of concerns about its accuracy in the systematic description of structural changes. In the present work, we focus on the improvement of the GLYCAM06 force field for β-d-glucose, a simple and the most abundant monosaccharide molecule, with the aid of machine learning techniques implemented with the TensorFlow library. Following the pre-sampling over a wide range of configuration space generated by MD simulation, the atomic charge and dihedral angle parameters in the GLYCAM06 force field were re-optimized to accurately reproduce the relative energies of β-d-glucose obtained by the density functional theory (DFT) calculations according to the structural changes. The validation for the newly proposed force-field parameters was then carried out by verifying that the relative energy errors compared to the DFT value were significantly reduced and that some inconsistencies with experimental (e.g., NMR) results observed in the GLYCAM06 force field were resolved relevantly.

Electronic, Vibrational, and Structural Study of Polysaccharide Agar-Agar Biopolymer

Polysaccharide biopolymer Agar-Agar extracted from red algae is a natural and biodegradable polymer. It is a combination of agarose (a neutral and linear polymer, with repeated units of agarobiose) and a heterogeneous mixture of agaropectin (a charged sulfated polymer). In this study, a comparative study of structural vibrational and electrochemical properties of agar-agar biopolymer with two different methods HF (Hartree-Fock) and DFT (Density Functional Theory) using a basis set 631+G (d, p) is performed. The comparative structural study of agar-agar biopolymer by HF and DFT method has been carried out to calculate the stability of the molecule. The thermionic properties and Mulliken charge distribution are analysed to deliver a quantitative study of partial atomic charge distribution. The overall vibrational analysis of primal modes of the biopolymer has been studied using FTIR analysis. Based on highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) composition and energies, various chemical parameters of the biopolymer have been evaluated. The Physico-chemical properties of this polysaccharide show a strong correlation with its optimized structure. Agar-agar has its application in the electrochemical, biotechnological, and pharmaceutical fields, as a stabilizer and gelling material.