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 (R²_Train) and R² values for the test set (R²_Test), 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.

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 (Q²_LOO) of 0.6584 and 0.6289, respectively.

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 (ESP_min), and volume (V) descriptors. Furthermore, the validity of the proposed model is corroborated by an adsorption study on an iron surface Fe(110).

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 Fe_n (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 β 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.

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 (λ_max) 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 (Q²_LOO) 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.

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 ΔG_b were determined at 93.58 kJ mol^-1, 0.378 kJ mol^-1 K^-1 and -19.17 ± 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 β-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.

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 E_gap(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 E_{gap(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.

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.

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

The Ir(i) complexes [Tp^Me2Ir(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 Tp^Me2Ir-(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.

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 β-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.