A DFT Study of the Reaction of Acrylamide with L-Cysteine and L-Glutathione.

Thermal processing of certain foods implies the formation of acrylamide, which has been proven to provoke adverse effects on human health. Thus, several strategies to mitigate it have been developed. One of them could be the application of organosulfur compounds obtained from natural sources to react with the acrylamide, forming non-toxic adducts. A DFT study of the acrylamide reaction with the organosulfur model compounds L-cysteine and L-glutathione by Michael addition and a free radical pathway complemented by a kinetic study of these model molecules has been applied. The kinetic evaluation results demonstrate that the L-glutathione reaction exhibited a higher rate constant than the other studied compound.

QSTR Modeling to Find Relevant DFT Descriptors Related to the Toxicity of Carbamates.

Compounds containing carbamate moieties and their derivatives can generate serious public health threats and environmental problems due their high potential toxicity. In this study, a quantitative structure-toxicity relationship (QSTR) model has been developed by using one hundred seventy-eight carbamate derivatives whose toxicities in rats (oral administration) have been evaluated. The QSRT model was rigorously validated by using either tested or untested compounds falling within the applicability domain of the model. A structure-based evaluation by docking from a series of carbamates with acetylcholinesterase (AChE) was carried out. The toxicity of carbamates was predicted using physicochemical, structural, and quantum molecular descriptors employing a DFT approach. A statistical treatment was developed; the QSRT model showed a determination coefficient (R2) and a leave-one-out coefficient (Q2LOO) of 0.6584 and 0.6289, respectively.

Mechanosynthesis of Photochromic Oligophenyleneimines: Optical, Electrochemical and Theoretical Studies.

In this work, two oligophenyleneimines type pentamers with terminal aldehydes, designated as DAFCHO (4,4'-((((((2,5-bis(octyloxy)-1,4-phenylene)bis(methanylylidene))bis(azanyl ylidene))bis(9H-fluorene-7,2-diyl))bis(azanylylidene))bis(methanylylidene))bis(2,5-bis(octyloxy) benzaldehyde)) and FDACHO (4,4'-((((((2,5-bis(octyloxy)-1,4-phenylene)bis(methanylylidene))bis (azanylylidene))bis(4,1-phenylene))bis(azanylylidene))bis(methanylylidene))bis(2,5-bis(octyloxy) benzaldehyde)) were synthesized by mechanochemistry method using 2,5-bis(octyloxy) terephtal aldehyde and 2,7-diaminofluorene or 1,4-phenylenediamine. All compounds were spectroscopically characterized using ¹H and 13C-NMR, FT-IR and mass spectrometry MALDITOF. The optical properties of the compounds were analyzed by UV-vis spectroscopy using different solvents. We observed that DAFCHO and FDACHO exhibit interesting photochromic properties when they are dissolved in chloroform and exposed to sunlight for 3, 5 and 10 min. The value of the energy band gap was calculated from the absorption spectra without irradiation Egap(optical). It was 2.50 eV for DAFCHO in chloroform solution, and it decreased to 2.34 eV when it is in films. For FDACHO, it was 2.41 eV in solution and 2.27 eV in film. HOMO (Highest Occupied Molecular Orbital), LUMO (Lowest Unoccupied Molecular Orbital) and Egap(electrochemical) values were obtained by electrochemical studies. The results indicate that the compounds can be considered as organic semiconductors since their values are 2.35 eV for DAFCHO and 2.06 eV for FDACHO. The structural and electronic properties of the compounds were corroborated with a DFT (Density Functional Theory) study.

Determination of antibiotics in feedstuff samples by microemulsion electrokinetic chromatography using fullerene as additive.

A microemulsion electrokinetic chromatography method was developed for the simultaneous detection and quantification of ciprofloxacin, norfloxacin, sulfamethoxazole, tetracycline, and oxytetracycline in feedstuff samples. The BGE composition was optimized by applying a Taguchi parameter design and consisted of phosphate 30 mmol/L, Tween-80 0.01 mmol/L, and fullerene 3 µmol/L, and adjusted to pH 8.0; the addition of surfactant and fullerene modifies the mobility of the analytes improving their resolution. Theoretical studies showed π-π and van der Waals interactions between antibiotic molecules and fullerene used as a pseudostationary phase. Under optimal conditions, limits of detection ranged from 0.7 to 1.5 µg/g; the analytes were separated in less than 6 min. The methodology proposed is useful for controlling and monitoring antibiotic residues in feedstuff samples.

A new computational model for the prediction of toxicity of phosphonate derivatives using QSPR.

Structural and electronic properties of a series of 25 phosphonate derivatives were analyzed applying density functional theory, with the exchange-correlation functional PBEPBE in combination with the 6-311++G** basis set for all atoms. The chemical reactivity of these derivatives has been interpreted using quantum descriptors such as frontier molecular orbitals (HOMO, LUMO), Hirshfeld charges, molecular electrostatic potential, and the dual descriptor [[Formula: see text]]. These descriptors are directly related to experimental median lethal dose ([Formula: see text], expressed as its decimal logarithm [[Formula: see text]([Formula: see text]] through a multiple linear regression equation. The proposed model predicts the toxicity of phosphonates in function of the volume (V), the load of the most electronegative atom of the molecule (q), and the eigenvalue of the molecular orbital HOMO ([Formula: see text]. The obtained values in the internal validation of the model are: [Formula: see text]%, [Formula: see text]%, [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text]%. The toxicity of nine phosphonate derivatives used as test molecules was adequately predicted by the model. The theoretical results indicate that the oxygen atom of the O=P group plays an important role in the interaction mechanism between the phosphonate and the acetylcholinesterase enzyme, inhibiting the removal of the proton of the ser-200 residue by the his-440 residue.

Density Functional Theory and Electrochemical Studies: Structure-Efficiency Relationship on Corrosion Inhibition.

The relationship between structure and corrosion inhibition of a series of 30 imidazol, benzimidazol, and pyridine derivatives has been established through the investigation of quantum descriptors calculated with PBE/6-311++G**. A quantitative structure-property relationship model was obtained by examination of these descriptors using a genetic functional approximation method based on a multiple linear regression analysis. Our results indicate that the efficiency of corrosion inhibitors is strongly associated with aromaticity, electron donor ability, and molecular volume descriptors. In order to calibrate and validate the proposed model, we performed electrochemical impedance spectroscopy (EIS) studies on imidazole, 2-methylimidazole, benzimidazole, 2-chloromethylbenzimidazole, pyridine, and 2-aminopyridine compounds. The experimental values for efficiency of corrosion inhibition are in good agreement with the estimated values obtained by our model, thus confirming that our approach represents a promising and suitable tool to predict the inhibition of corrosion attributes of nitrogen containing heterocyclic compounds. The adsorption behavior of imidazole or benzimidazole heterocyclic molecules on the Fe(110) surface was also studied to elucidate the inhibition mechanism; the aromaticity played an important role in the adsorbate-surface complex.

Hydrodesulfurization of Dibenzothiophene: A Machine Learning Approach.

The hydrodesulfurization (HDS) process is widely used in the industry to eliminate sulfur compounds from fuels. However, removing dibenzothiophene (DBT) and its derivatives is a challenge. Here, the key aspects that affect the efficiency of catalysts in the HDS of DBT were investigated using machine learning (ML) algorithms. The conversion of DBT and selectivity was estimated by applying Lasso, Ridge, and Random Forest regression techniques. For the estimation of conversion of DBT, Random Forest and Lasso offer adequate predictions. At the same time, regularized regressions have similar outcomes, which are suitable for selectivity estimations. According to the regression coefficient, the structural parameters are essential predictors for selectivity, highlighting the pore size, and slab length. These properties can connect with aspects like the availability of active sites. The insights gained through ML techniques about the HDS catalysts agree with the interpretations of previous experimental reports.

Conceptual DFT, machine learning and molecular docking as tools for predicting LD50 toxicity of organothiophosphates.

CONTEXT: Several descriptors from conceptual density functional theory (cDFT) and the quantum theory of atoms in molecules (QTAIM) were utilized in Random Forest (RF), LASSO, Ridge, Elastic Net (EN), and Support Vector Machines (SVM) methods to predict the toxicity (LD50) of sixty-two organothiophosphate compounds. The A-RF-G1 and A-RF-G2 models were obtained using the RF method, yielding statistically significant parameters with good performance, as indicated by R2 values for the training set (R2Train) and R2 values for the test set (R2Test), around 0.90. METHODS: The molecular structure of all organothiophosphates was optimized via the range-separated hybrid functional ωB97XD with the 6-311 + + G** basis set. Seven hundred and eighty-seven descriptors have been processed using a variety of machine learning algorithms: RF LASSO, Ridge, EN and SVM to generate a predictive model. The properties were obtained with Multiwfn, AIMALL and VMD programs. Docking simulations were performed by using AutoDock 4.2 and LigPlot + programs. All the calculations in this work are carried out in Gaussian 16 program package.

Assessment of Simultaneous Global Optimization of Geometry and Total Spin of Small Iron Clusters.

In this work, simultaneous global optimization of geometry and total spin of small iron clusters Fen (3 ≤ n ≤ 40) is assessed using Simulated Annealing (SA) simulations with forces calculated at the DFT-based Tight-Binding (DFTB) level of theory. In order to optimize the total spin, the occupancies of α and ß densities were allowed to relax at each SA step, resulting in a continuous variation of the total spin along the trajectory. The behavior and performance of the procedure were investigated running two series of 10 independent "long" molecular dynamics simulations and one series of 100 independent "short" simulations. Cluster structures optimized with the assessed methodology reproduced geometries and magnetic moments reported in a previous work very well where multiple fixed total spin and geometries of iron clusters were individually probed, and for some clusters, more stable global minima were found. Other properties such as binding energies and second energy differences were also calculated in order to compare with previously reported theoretical and experimental values. The few mismatches were found to be driven by quasi degenerated ground states with different magnetic moments or by states with crossing free energies at high temperatures.

New QSPR model for prediction of corrosion inhibition using conceptual density functional theory.

The relationship between structure and corrosion inhibition of a series of twenty-eight quinoline and pyridine derivatives has been established through the investigation of quantum descriptors calculated with PBE/6-311 + + G** method. A quantitative structure-property relationship (QSPR) model was obtained by examining these descriptors using a genetic algorithm approximation method based on a multiple linear regression analysis. The results indicate that the efficiency of corrosion inhibitors is strongly associated with hardness (η), minimal electrostatic potential (ESPmin), and volume (V) descriptors. Furthermore, the validity of the proposed model is corroborated by an adsorption study on an iron surface Fe(110).

Effects of bentonite on p-methoxybenzyl acetate: a theoretical model for oligomerization via an electrophilic-substitution mechanism.

Tonsil Actisil FF, a commercial bentonitic clay, promotes the formation of a series of electrophilic-aromatic-substitution products from para-methoxybenzyl acetate in carbon disulfide. The molecules obtained correspond to linear isomeric dimers, trimers, tetramers and a pentamer, according to their spectroscopic data. A clear indication of the title mechanistic pathway for the oligomerization growth was obtained from the analysis of a set of computational-chemistry calculations using the density-functional-theory level B3LYP/6-311++G(d,p). The corresponding conclusions were based on the computed dipole moments, the HOMO/LUMO distributions, and a natural-populations analysis of the studied molecules.

The chemical reactivity and QSPR of organic compounds applied to dye-sensitized solar cells using DFT.

The structural and electronic properties were calculated for seventy organic compounds used as dye sensitizers in solar cells, applying the B3LYP exchange-correlation energy functional with the 6-311G∗∗ basis set. Moreover, the present study proposes two new quantitative structure-property relationship (QSPR) models that enable the prediction of the power conversion efficiency (PCE) and maximum absorption wavelength (λmax) of these systems, the two QSPR models were validated using the coefficient of determination (R2) of 0.62 for both models with the leave-one-out cross-validation correlation coefficient (Q2LOO) of 0.55 and 0.57, respectively. Furthermore, applicability domain analysis was conducted in order to identify the related compounds via the extrapolation of the model.

Mathematical Models Generated for the Prediction of Corrosion Inhibition Using Different Theoretical Chemistry Simulations.

The use of corrosion inhibitors is an important method to retard the process of metallic attack by corrosion. The construction of mathematical models from theoretical-computational and experimental data obtained for different molecules is one of the most attractive alternatives in the analysis of corrosion prevention, whose objective is to define those molecular characteristics that are common in high-performance corrosion inhibitors. This review includes data of corrosion inhibitors evaluated in different media, the most commonly studied molecular descriptors, and some examples of mathematical models generated by different researchers.

Spectroscopic studies and molecular modelling of the aflatoxin M1-bovine α-lactalbumin complex formation.

Since the high incidence of aflatoxin M1 (AFM1) in milk and dairy products poses a serious risk to human health, this work aimed to investigate the complex formation between bovine α-lactalbumin (α-La) and AFM1 using different spectroscopic methods coupled with molecular docking studies. Fluorescence spectroscopy measurements demonstrated the AFM1 addition considerably reduced the α-La fluorescence intensity through a static quenching mechanism. The results indicated on the endothermic character of the reaction, and the hydrophobic interaction played a major role in the binding between AFM1 and α-La. The binding site stoichiometric value (n = 1.32) and a binding constant of 2.12 × 103 M-1 were calculated according to the Stern-Volmer equation. The thermodynamic parameters ΔH, ΔS and ΔGb were determined at 93.58 kJ mol-1, 0.378 kJ mol-1 K-1 and -19.17 ±â€¯0.96 kJ mol-1, respectively. In addition, far-UV circular dichroism studies revealed alterations in the α-La secondary structures when the α-La-AFM1 complex was formed. An increased content of the α-helix structures (from 35 to 40%) and the ß-sheets (from 16 to 19%) were observed. Furthermore, protein-ligand docking modelling demonstrated AFM1 could bind to the hydrophobic regions of α-La protein. Overall, the gathered results confirmed the α-La-AFM1 complex formation.

A theoretical and experimental approach to evaluate zein-calcium interaction in nixtamalization process.

The possible interactions between α-zein and Ca2+ in nixtamalization process were analyzed from a multidisciplinary approach, considering the effect of these interactions on the thermal properties of the nixtamalized flour. SDS-PAGE under reducing and non-reducing conditions did not reveal differences between patterns of zeins from nixtamalized and control samples. However, analysis from affinity capillary electrophoresis indicated an increment in protein volume when calcium is added to zein extracted from nixtamalized flour. In addition, the binding constant for the zein-calcium interaction was calculated indicating a higher affinity for calcium by zein from nixtamalized samples. Molecular dynamics simulations indicated that the interaction α-zein-Ca2+ through C-ter was more favorable than Glu48. However, in excess of Ca2+ ions, each site could bind one calcium atom at the same time, confirming that aggregation of α-zein through calcium bridges is possible, expanding the technological applications of this protein.

Electrochemical and theoretical studies of the interactions of a pyridyl-based corrosion inhibitor with iron clusters (Fe15, Fe30, Fe45, and Fe60).

The capacity of 2,6-bis[((2-pyridylmethyl)oxy)methyl)]pyridine (BPMMP) to inhibit the corrosion of mild carbon steel in HCl was analyzed. In a polarization study, both the cathodic and anodic currents were appreciably decreased in the presence of BPMMP, suggesting that this ligand is effective at inhibiting corrosion at the metal surface. This conclusion is consistent with the results of impedance analysis, where only one time constant corresponding to one depressed capacitive loop was detected, and the diameter of the impedance plot was directly related to the concentration of BPMMP. Furthermore, when recurrence analysis was performed, a decrease in regular noise was observed due to the change of Shannon entropy when the inhibitor was present in the corrosive medium, showing that a high degree of recurrence increases the entropy of the system. Electrochemical data on some pyridyl-based inhibitors were collected from the literature and used to plot (i) I corr (A/cm2) vs. inhibition efficiency (η%) and (ii) ΔG°ads vs. inhibition efficiency (ƞ%) in order to examine the general relationships between these parameters. Furthermore, the interactions of the ligand BPMMP with different iron clusters (Fe15, Fe30, Fe45, and Fe60) were analyzed theoretically using density functional theory (DFT). The structural and electronic properties of BPMMP and its protonated form BPMMPH+ were studied before and after the interactions of BPMMP with the iron clusters. The first protonation was found to occur at pyridine nitrogen atom N1, resulting in a Gibbs free energy ΔG of -10.2 kcal/mol, with an energy difference of 5.3 kcal/mol between the two possible protonated conformers. Graphical abstract Recurrence and Noise signal performance of BPMMP as corrosion inhibitor.

Reduced density gradient as a novel approach for estimating QSAR descriptors, and its application to 1, 4-dihydropyridine derivatives with potential antihypertensive effects.

The relationship between the chemical structure and biological activity (log IC50) of 40 derivatives of 1,4-dihydropyridines (DHPs) was studied using density functional theory (DFT) and multiple linear regression analysis methods. With the aim of improving the quantitative structure-activity relationship (QSAR) model, the reduced density gradient s( r) of the optimized equilibrium geometries was used as a descriptor to include weak non-covalent interactions. The QSAR model highlights the correlation between the log IC50 with highest molecular orbital energy (E HOMO), molecular volume (V), partition coefficient (log P), non-covalent interactions NCI(H4-G) and the dual descriptor [Δf(r)]. The model yielded values of R 2=79.57 and Q 2=69.67 that were validated with the next four internal analytical validations DK=0.076, DQ=-0.006, R P =0.056, and R N=0.000, and the external validation Q 2boot=64.26. The QSAR model found can be used to estimate biological activity with high reliability in new compounds based on a DHP series. Graphical abstract The good correlation between the log IC50 with the NCI (H4-G) estimated by the reduced density gradient approach of the DHP derivatives.

Activation of aldehydes by exocyclic iridium(i)-η4:π2-diene complexes derived from 1,3-oxazolidin-2-ones.

The Ir(i) complexes [TpMe2Ir(η4-1,4-diene)] 2b and 2c react thermally with a variety of aromatic aldehydes, 3a-e, to generate the metallabicyclic compounds 4e-k and the Fischer-type carbenes 5a-b in moderate yields. These reactions are proposed to take place with the initial formation of η1-aldehyde adducts as key intermediates. The formation of the metallabicyclic compounds 4e-k involves a formal decarboxylation process at the exo-2-oxazolidinone diene and an ortho metallation of the aromatic ring. The generation of the Fischer-type carbenes 5a-b is the result of a series of metal-based rearranged intermediates with no decarboxylation observed. Treatment of the η4-diene complex 2b with a variety of Lewis bases induces a change in the binding mode of the diene ligand from η4:π2 to η2:σ2 to form the Ir(iii) derivatives 6b-d of composition TpMe2Ir-(η4:π2-1,4-diene)(L) (L = CO, MeCN, and C5H5N). A study of reactions of complex 2b with either mono- or poly-deuterated aldehydes was performed to understand the mechanisms of such processes. The results of these studies were used to determine plausible formation mechanisms of the metallabicyclic compounds 4e-4k and Fischer-type carbenes 5a-b compound series. These mechanisms were corroborated by density functional theory (DFT) calculations of the free energy profiles.

Theoretical and experimental studies of phenol oxidation by ruthenium complex with N,N,N-tris(benzimidazol-2yl-methyl)amine.

The ruthenium complex with (N,N,N-tris(benzimidazol-2yl-methyl)amine, L(1)) was prepared, and characterized. Fukui data were used to localize the reactive sites on the ligand. The structural and electronic properties of the complex were analyzed by DFT in different oxidation states in order to evaluate its oxidant properties for phenol oxidation. The results show that the hard Ru(IV) cation bonds preferentially with a hard base (Namine = amine nitrogen, or axial chloride ion), and soft Ru(II) with a soft base (Nbzim = benzimidazole nitrogen or axial triphenyl phosphine). Furthermore, the Jahn-Teller effect causes an elongation of the axial bond in the octahedral structure. The bonding nature and the orbital contribution to the electronic transitions of the complex were studied. The experimental UV-visible bands were interpreted by using TD-DFT studies. The complex oxidizes phenol to benzoquinone in the presence of H2O2 and the intermediate was detected by HPLC and (13)C NMR. A possible mechanism and rate law are proposed for the oxidation. The adduct formation of phenol with [Ru(O)L(1)](2+) or [Ru(OH)L(1)](+) is theoretically analyzed to show that [Ru(OH)L(1)-OPh](+) could produce the phenol radical.

Synthesis of Ir(III) complexes with Tp(Me2) and acac ligands and their reactivity with electrophiles.

The reaction of the bis(ethylene) complex [Tp(Me2)Ir(C2H4)2] () (Tp(Me2) = hydrotris(3,5-dimethylpyrazolyl)borate) with an excess of 2,4-pentanedione (acetylacetone, Hacac) at 70 °C produced a mixture of the Ir(iii) complex [Tp(Me2)Ir(acac)(C2H5)] () as a major product (67% yield) and two other side complexes [Tp(Me2)Ir(acac)(H)] () and [Tp(Me2)Ir(C9H14O2)] () in 20 and 13% yields, respectively. According to the proposed reaction mechanism and DFT calculations, complexes and are generated from an 18e(-) intermediate [Tp(Me2)Ir(C2H4)(acac)(C2H3)] () which undergoes either hydrogen insertion or ß-hydride elimination followed by the subsequent loss of a molecule of ethylene. The lowest yielding complex which features a 2-iridafuran is presumably generated from an unusual thermal coupling between one vinylic and one acac moiety. The availability of the acidic α-proton of the acac ligand was tested by the treatment of complex with Br2 and Cu(NO3)2 rendering the substitution complexes [Tp(3-Br,Me2)Ir(3-Br-acac)Br] () and [Tp(Me2)Ir(3-NO2-acac)(C2H5)] () in good yields. The series of heteroleptic iridium(iii) compounds display air and moisture stability and have been characterized by NMR, IR, and elemental analyses, and, in the case of , and , by single-crystal X-ray diffraction analyses.