Conductor-like Polarizable Continuum Research Articles

Computational-based investigation of antioxidative potential polyphenolic compounds of Salvia officinalis L.: combined DFT and molecular docking approaches.

The antioxidant properties of the three polyphenolic compounds (carnosol, cirsiliol, and luteolin) of Salvia officinalis L. were investigated employing the density functional theory (DFT) calculations at the B3LYP of basis set at 6-311 + + G (d, p) in order to evaluate their antioxidant activity. The enthalpies of reactions associated with the SET-PT, SPLET, and HAT mechanisms were analyzed in gas and in different solvents using the CPCM (conductor-like polarizable continuum) model. For all possible hydrogen donor sites, the corresponding parameters (BDE, AIP, PDE, PA, ETE, HOMOs, and LUMOs) and reactivity indices (IPE, EA, Χ, η, S, and ω) were also evaluated. The calculated results showed that derivatives 12-OH, 11-OH, 4'-OH, and 3'-OH had the lowest antioxidant activity. The results showed as well that carnosol, cirsiliol, and luteolin have higher reactivity compared to ascorbic acid and could be considered better antioxidants. According to research, the catechol group is crucial in influencing the studied compounds antioxidant activity. The theoretically predicted order of antioxidant efficiencies in this work agrees well with the QSAR (quantitative structure-activity relationship) data. The findings show that in the vacuum as well as benzene media. HAT would be the most effective mechanism; in contrast, the thermodynamic equilibrium approach in polar media is the SPLET mechanism. Likewise, the outcomes of the docking modeling confirm that the selected molecules have high inhibitory activity to glutathione-S-transferases (GSTs) receptors. Moreover, they have very important pharmacokinetic, chemical, and biological profiles. Finally, all the results show that the three natural molecules have good pharmacokinetic profiles, particularly the bioavailability and permeability toward biological membranes. The software packages used in this investigation are Gaussian 16, Discovery studio Visualizer, and AutoDock vina. The three compounds (carnosol, cirsiliol, and luteolin) of Salvia officinalis L. were optimized with DFT/B3LYP of basis set at 6-311 + + G (d, p). The optimized structures were established via vibrational analysis (i.e., no imaginary frequencies in the frequency set). All enthalpies were zero-point (ZPE) corrected. Vibrational frequency calculations were performed at 298.15K and 1 atmosphere pressure to determine the thermodynamic characteristics of the investigated reactions. The descriptors were associated with the antioxidant mechanisms for investigated molecules in vacuum and in various solvents. The molecular docking was used by AutoDock vina to estimate and evaluate the title compounds compatibility as potential antioxidant drugs utilizing appropriate receptor proteins. The solvation effect in the medium of benzene (ɛ = 2.27) and water (ɛ = 78.39) was taken into account. Furthermore, a methanol solvent (ɛ = 32.61) was also taken into consideration to compare with the empirical data.

Novel 1,3,4-oxadiazole linked benzopyrimidinones conjugates: Synthesis, DFT study and antimicrobial evaluation

This work describes the synthesis, characterization and antimicrobial evaluation of a series of new 1,3,4-oxadiazole linked benzopyrimidinones. Their structures were confirmed on the basis of 1H, 13C NMR and ES-HRMS analysis. Their molecular geometry are also studied theoretically by the Density Functional Theory (DFT) method with B3LYP/6–31++G (d,p). All the calculations were done in DMSO, using conductor like polarizable continuum (CPCM). The target compounds were screened for their antimicrobial activity against four types of pathogenic bacteria and three fungal strains. Biological results revealed that some of these compounds demonstrated excellent to moderate antimicrobial activities with minimum inhibitory concentration (MIC) values ranging from 10.8 to 140.7 μM. Notably, compounds 5g and 5h showed the highest inhibitory activity against all bacterial strains with MIC values ranging from 111.3 to 10.8 μM against S. aureus, E. coli and P. aeruginosa, and displayed a good antifungal activity against C. albicans with MIC values of 10.8 and 27,8 μM, respectively. The structure-activity relationship (SAR) was discussed.

UV-vis absorption spectra of Sn(IV)tetrakis(4-pyridyl) porphyrins on the basis of axial ligation and pyridine protonation.

The present study highlights the structural and electronic spectra of Sn(IV)tetrakis(4-pyridyl) porphyrins (SnTP) using density functional theory (DFT) and time-dependent density functional theory (TDDFT). The impact of axial ligands (OH-, Cl-, and H2O) and protonation at pyridine sites on the excitation properties of SnTP is also explored. The considered SnTPs were optimized at B3LYP/6-31+G* level of theory with LANL2DZ basis set for Sn metal. The effects of tetrahydrofuran (THF) and dimethylformamide (DMF) solvents were also assessed employing conductor-like polarizable continuum (C-PCM) model. The observed structural effects correlate well with the experimental data and clearly depict the impact of axial ligands on the SnTP ring. The absorption spectra along with the frontier orbitals in all three phases show noticeable dependence of axial ligation on the photophysical properties of SnTPs. The transition character of molecular orbitals and their respective density of states (DOS) were explored to infer the orbitals involved in electronic transitions. Graphical abstract The structural and electronic spectra of Sn(IV)tetrakis(4-pyridyl) porphyrins (SnTP) were examined using time-dependent density functional theory (TDDFT). Axial ligation and pyridine protonation significantly affects the absorption properties of Sn complexes. The overall results suggest the application of [(OH-)Sn (OH-)TP] and [(Cl-)Sn (Cl-)TP] as photosensitizers.

Theoretical and experimental study of the reaction of 2-guanidinobenzimidazole on a series of meta-substituted benzaldehydes

The syntheses of a variety of 1,3,5-triazinebenzimidazoles obtained by the cyclocondensation reaction of 2-guanidinobenzimidazole with a series of meta-substituted benzaldehydes were reported. The prepared compounds were fully characterized by IR and NMR spectroscopies. Based on the density functional theory(DFT) calculations method, quantum chemical calculations were performed by Gaussian 09 set of programs. All possible transition states, reactants and products were fully optimized at the hybrid density functional B3LYP level using the 6-311+G(d,p). The geometries of five possible tautomers of 2-amino-4-aryl[1,3,5]triazino[1,2-a]benzimidazoles were optimized in ethanol, using conductor like polarizable continuum(CPCM) in the gas phase. The energetic diagrams of tautomeric equilibrium showed that form A is the most stable tautomer which proved to be in accordance with the X-ray diffraction structure analysis. In order to interpret the reaction mechanism, the chemical reactivity was studied using local and global reactivity indexes.

Effect of Substituents on the Preferred Modes of One-Electron Reductive Cleavage of N–Cl and N–Br Bonds

In this study, we investigate the effect of substituents in determining the modes of one-electron reductive cleavage of X-NRR' (X = Cl and Br) molecules. We achieve this through comparison of the calculated gas-phase electron affinities (EAs) and aqueous-phase one-electron reduction potentials (E°'s) for a range of nitrogen-centered radicals ((•)NRR') with the corresponding EA and E° values for (•)Cl and (•)Br. The gas-phase EAs have been obtained using the benchmark-quality W1w thermochemical protocol, whereas E° values have been obtained by additionally applying free energy of solvation corrections, obtained using the conductor-like polarizable continuum (CPCM) model. We find that the N-halogenated derivatives of amines and amides should generally cleave in such a way as to afford (•)NRR' and X(-). For the N-halogenated imides, on the other hand, the N-brominated derivatives are predicted to produce (•)Br in solution, whereas the N-chlorinated derivatives again would give Cl(-). Importantly, we predict that N-bromouracil is likely to afford (•)Br. This may have important implications in terms of inflammatory-related diseases, because (•)Br may damage biomolecules such as proteins and DNA. To assist in the determination of the gas-phase EAs of larger (•)NRR' radicals, not amenable to investigation using W1w, we have evaluated the performance of a wide range of lower-cost theoretical methods. Of the standard density functional theory (DFT) procedures, M06-2X, τ-HCTHh, and B3-LYP show good performance, with mean absolute deviations (MADs) from W1w of 4.8-6.8 kJ mol(-1), whereas ROB2-PLYP and B2-PLYP emerge as the best of the double-hybrid DFTs (DHDFTs), with MADs of 2.5 and 3.0 kJ mol(-1), respectively. Of the Gn-type procedures, G3X and G4 show very good performance (MADs = 2.4 and 2.6 kJ mol(-1), respectively). The G4(MP2)-6X+ procedure performs comparably, with an MAD of 2.7 kJ mol(-1), with the added advantage of significantly reduced computational expense.

On the combined use of discrete solvent models and continuum descriptions of solvent effects in ligand exchange reactions: a case study of the uranyl(VI) aquo ion

Modeling of the solvent is important when using quantum chemical methods for the assignment of mechanisms from experimental studies of the exchange of water between metal aquo ions and the bulk solvent. In the present study, we have investigated if and how the mechanisms for water exchange in the UO2(OH2)52+–H2O system is affected by the choice of chemical models for the second coordination sphere and physical models for describing the cavity in conductor-like polarizable continuum (CPCM) models. In the first case, we have compared models with one and five waters in the second coordination sphere. For both models, we have compared cavities in which each atom is assigned one spherical cavity and one in which the water molecules are described by a single spherical cavity (the United Atom model). There are significant differences in the relative energy of dissociative and associative intermediates; however, they are not large enough to affect the conclusion that the water exchange proceeds through an associative/interchange mechanism.

Electronic structures and spectroscopic properties of rhenium (I) tricarbonyl photosensitizer: [Re(4,4′-(COOEt) 2-2,2′-bpy)(CO) 3py]PF 6

The ground state and lowest triplet-state structures of [Re(4,4′-(COOEt) 2-2,2′-bpy)(CO) 3py]PF 6 photosensitizer (bpy = bipyridine, py = pyridine) have been studied with density functional theory (DFT). Time-dependent density functional theory (TD-DFT) was carried out to predict the photophysical properties of the photosensitizer. The effects of the solvents were evaluated using the conductor-like polarizable continuum (CPCM) method in dichloromethane, chloroform, acetonitrile, acetone, ethanol and dimethylsulfoxide. The electronic transition energies computed with BLYP, MPWPW91, B3LYP and MPW1PW91 functionals are compared with the experimental spectra. Based on the calculated excited energies, the experimental absorption maximum is assigned as metal-to-ligand charge transfer (MLCT) and ligand-to-ligand charge transfer (LLCT) mixed transition, and the luminescence originates from the lowest triplet state that is ascribed as the mixed transition of MLCT/LLCT.

Chelate effect and thermodynamics of metal complex formation in solution: a quantum chemical study.

The accuracy of quantum chemical predictions of structures and thermodynamic data for metal complexes depends both on the quantum chemical methods and the chemical models used. A thermodynamic analogue of the Eigen-Wilkins mechanism for ligand substitution reactions (Model A) turns out to be sufficiently simple to catch the essential chemistry of complex formation reactions and allows quantum chemical calculations at the ab initio level of thermodynamic quantities both in gas phase and solution; the latter by using the conductor-like polarizable continuum (CPCM) model. Model A describes the complex formation as a two-step reaction: 1. [M(H2O)x](aq) + L(aq) <==>[M(H2O)x], L(aq); 2. [M(H2O)x], L(aq) <==>[M(H2O)(x-1)L],(H2O)(aq). The first step, the formation of an outer-sphere complex is described using the Fuoss equation and the second, the intramolecular exchange between an entering ligand from the second and water in the first coordination shell, using quantum chemical methods. The thermodynamic quantities for this model were compared to those for the reaction: [M(H2O)x](aq) + L(aq) <==>[M(H2O)(x-1)L](aq) + (H2O)(aq) (Model B), as calculated for each reactant and product separately. The models were tested using complex formation between Zn(2+) and ammonia, methylamine, and ethylenediamine, and complex formation and chelate ring closure reactions in binary and ternary UO(2)(2+)-oxalate systems. The results show that the Gibbs energy of reaction for Model A are not strongly dependent on the number of water ligands and the structure of the second coordination sphere; it provides a much more precise estimate of the thermodynamics of complex formation reactions in solution than that obtained from Model B. The agreement between the experimental and calculated data for the formation of Zn(NH(3))(2+)(aq) and Zn(NH(3))(2)(2+)(aq) is better than 8 kJ/mol for the former, as compared to 30 kJ/mol or larger, for the latter. The Gibbs energy of reaction obtained for the UO(2)(2+) oxalate systems using model B differs between 80 and 130 kJ/mol from the experimental results, whereas the agreement with Model A is better. The errors in the quantum chemical estimates of the entropy and enthalpy of reaction are somewhat larger than those for the Gibbs energy, but still in fair agreement with experiments; adding water molecules in the second coordination sphere improves the agreement significantly. Reasons for the different performance of the two models are discussed. The quantum chemical data were used to discuss the microscopic basis of experimental enthalpy and entropy data, to determine the enthalpy and entropy contributions in chelate ring closure reactions and to discuss the origin of the so-called "chelate effect". Contrary to many earlier suggestions, this is not even in the gas phase, a result of changes in translation entropy contributions. There is no simple explanation of the high stability of chelate complexes; it is a result of both enthalpy and entropy contributions that vary from one system to the other.