Computational prediction of retention times of veterinary antibiotics obtained by liquid chromatography-mass spectrometry.

BACKGROUND: Veterinary antibiotics are chemical compounds used to kill or inhibit the growth of pathogenic bacteria associated with animal diseases. These molecules can be defined by their retention times (tR) in liquid chromatography-mass spectrometry (LC-MS). One strategy to predict the tR of new veterinary antibiotics is the development of predictive quantitative structure-property relationships (QSPRs), which were used in this study. RESULTS: A database of 122 antibiotics was selected in which the tR was measured using a Hypersil GOLD column. An optimal three-feature model was developed by integrating the unsupervised variable reduction, replacement method variable subset selection, and multiple linear regression. The negligible differences among the coefficient of determination and the root-mean-square error for the training set (R2 = 0.902 and RMSEC = 0.871) and test set (Q2 = 0.854 and RMSEP = 1.064) indicate a stable and predictive model. In a further step, a more in-depth explanation of the mechanism of action of each descriptor in predicting the tR is provided, with the construction of the theoretical chemical space for accurate predictions of new antibiotics. CONCLUSION: The in silico model developed in this work identified three molecular descriptors associated with aqueous solubility, octanol-water partition coefficient, and the presence of negative and lipophilic atom pairs. The QSPR developed here could be implemented by agricultural and food chemists to identify and monitor existing and new antibiotics within the framework of LC-MS. The computational model was developed in accordance with five principles outlined by the Organization for Economic Co-operation and Development. © 2024 Society of Chemical Industry.

Chemoinformatic modelling of the antioxidant activity of phenolic compounds.

BACKGROUND: Antioxidants are chemicals used to protect foods from deterioration by neutralizing free radicals and inhibiting the oxidative process. One approach to investigate the antioxidant activity is to develop quantitative structure-activity relationships (QSARs). RESULTS: A curated database of 165 structurally heterogeneous phenolic compounds with the Trolox equivalent antioxidant capacity (TEAC) was developed. Molecular geometries were optimized by means of the GFN2-xTB semiempirical method and diverse molecular descriptors were obtained afterwards. For model development, V-WSP unsupervised variable reduction was used before performing the genetic algorithms-variable subset selection (GAs-VSS) to construct the best five-descriptor multiple linear regression model. The coefficient of determination and the root mean square error were used to measure the performance in calibration (R2 = 0.789 and RMSEC = 0.381), and test set prediction (Q2 = 0.748 and RMSEP = 0.416), along several cross-validation criteria. To thoroughly understand the TEAC prediction, a fully explained mechanism of action of the descriptors is provided. In addition, the applicability domain of the model defined a theoretical chemical space for reliable predictions of new phenolic compounds. CONCLUSION: This in silico model conforms to the five principles stated by the Organisation for Economic Co-operation and Development. The model might be useful for virtual screening of the antioxidant chemical space and for identifying the most potent molecules related to an experimental measurement of TEAC activity. In addition, the model could assist chemists working on computer-aided drug design for the synthesis of new targets with improved activity and potential uses in food science. © 2023 Society of Chemical Industry.

Anticancer activity of a new copper(II) complex with a hydrazone ligand. Structural and spectroscopic characterization, computational simulations and cell mechanistic studies on 2D and 3D breast cancer cell models.

We report here the synthesis, crystal structure, characterization and anticancer activity of a copper(ii)-hydrazone complex, [Cu(MeBHoVa)(H2O)2](NO3) (for short, CuHL), against human breast cancer cells on monolayer (2D) and spheroids/mammospheres (3D). The solid-state molecular structure of the complex has been determined by X-ray diffraction methods. The conformational space was searched and geometries were optimized both in the gas phase and including solvent effects by computational methods based on DFT. The compound has been characterized in the solid state and in solution by spectroscopic (FTIR, Raman, UV-vis) methods. The results were compared with those obtained for the hydrazone ligand and complemented with DFT calculations. Cell viability assays on MCF7 (IC50(CuHL) = 1.7 ± 0.1 µM, IC50(CDDP) = 42.0 ± 3.2 µM) and MDA-MB-231 (IC50(CuHL) = 1.6 ± 0.1 µM, IC50(CDDP) = 131.0 ± 18 µM) demonstrated that the complex displays higher antitumor activity than cisplatin (CDDP) on 2D and 3D human breast cancer cell models. Molecular docking and molecular dynamics simulations showed that CuHL could interacts with DNA, inducing a significant genotoxic effect on both breast cancer cells from 0.5 to 1 µM. On the other hand, CuHL increases the ROS production and induces cell programmed death on breast cancer cells at very low micromolar concentrations (0.5-1.0 µM). Moreover, the compound decreased the amount of breast CSCs on MCF7 and MDA-MB-231 cells reducing the percentage of CD44+/CD24-/low cells from 0.5 to 1.5 µM. In addition, CuHL overcame CDDP with an IC50 value 65-fold lower against breast multicellular spheroids ((IC50(CuHL) = 2.2 ± 0.3 µM, IC50(CDDP) = 125 ± 4.5 µM)). Finally, CuHL reduced mammosphere formation capacity, hence affecting the size and number of mammospheres and showing that the complex exhibits antitumor properties on monolayer (2D) and spheroids (3D) derived from human breast cancer cells.

Quantitative structure-property relationship analysis for the retention index of fragrance-like compounds on a polar stationary phase.

A quantitative structure-property relationship (QSPR) was developed for modeling the retention index of 1184 flavor and fragrance compounds measured using a Carbowax 20M glass capillary gas chromatography column. The 4885 molecular descriptors were calculated using Dragon software, and then were simultaneously analyzed through multivariable linear regression analysis using the replacement method (RM) variable subset selection technique. We proceeded in three steps, the first one by considering all descriptor blocks, the second one by excluding conformational descriptor blocks, and the last one by analyzing only 3D-descriptor families. The models were validated through an external test set of compounds. Cross-validation methods such as leave-one-out and leave-many-out were applied, together with Y-randomization and applicability domain analysis. The developed model was used to estimate the I of a set of 22 molecules. The results clearly suggest that 3D-descriptors do not offer relevant information for modeling the retention index, while a topological index such as the Randic-like index from reciprocal squared distance matrix has a high relevance for this purpose.

Structural, spectroscopic and DFT study of 4-methoxybenzohydrazide Schiff bases. A new series of polyfunctional ligands.

Five Schiff bases obtained from condensation of 4-methoxybenzohydrazide with related aldehydes, namely o-vanillin, vanillin, 5-bromovanillin, 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde were prepared. A detailed structural and spectroscopic study is reported. The crystal structures of four members of the family were determined and compared with one another. The hydrazones obtained from 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde resulted to be isomorphic to each other. The solid-state structures are stabilized by intra-molecular O-H⋯N interactions in salicylaldehyde derivatives between the O-H moiety from the aldehyde and the hydrazone nitrogen atom. All crystals are further stabilized by inter-molecular H-bonds mediated by the crystallization water molecule. A comparative analysis between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. The structure is predicted for the compound for which the crystal structure was not determined. Infrared and electronic spectra were measured and assigned with the help of data obtained from computational methods based on the Density Functional Theory.

Determining the molecular basis for the pH-dependent interaction between 2'-deoxynucleotides and 9H-pyrido[3,4-b]indole in its ground and electronic excited states.

Interaction between norharmane and three different 2'-deoxynucleotides (dNMP) (2'-deoxyguanosine 5'-monophosphate (dGMP), 2'-deoxyadenosine 5'-monophosphate (dAMP) and 2'-deoxycytidine 5'-monophosphate (dCMP)), in aqueous solution, was studied in the ground state by means of UV-vis and (1)H-NMR spectroscopy and in the first electronic excited state using steady-state and time-resolved fluorescence spectroscopy. In all cases, the norharmane-dNMP interaction dependence on the pH was examined. Possible mechanisms for the interaction of both ground and electronic excited states of norharmane with nucleotides are discussed. Spectroscopic, molecular modeling and chemometric analysis were performed to further characterize the chemical structure of the complexes formed and to get additional information concerning the interaction between dNMPs and norharmane.

An experimental and DFT study of a disulfide-linked Schiff base: synthesis, characterization and crystal structure of bis (3-methoxy-salicylidene-2-aminophenyl) disulfide in its anhydrous and monohydrate forms.

A detailed structural and spectroscopic study of the disulfide Schiff base obtained from condensation of 2-aminothiophenol and o-vanillin is reported. It includes the analyses of the anhydrous and monohydrate forms of the title compound. Structures of both solids were resolved by X-ray diffraction methods. A comparison between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. Vibrational (IR and Raman) and electronic spectra were measured and assigned with the help of computational methods based on the Density Functional Theory. Calculated MEP-derived atomic charges were calculated to predict coordination sites for metal complexes formation.

Computational chemical analysis of unconjugated bilirubin anions and insights into pKa values clarification.

The pKa, the negative logarithm of the acid dissociation equilibrium constant, of the carboxylic acid groups of unconjugated bilirubin in water is a discussed issue because there are quite different experimental values reported. Using quantum mechanical calculations we have studied the conformational behavior of unconjugated bilirubin species (in gas phase and in solution modeled implicitly and explicitly) to provide evidence that may clarify pKa values because of its pathophysiological relevance. Our results show that rotation of carboxylate group, which is not restricted, settles it in a suitable place to establish stronger interactions that stabilizes the monoanion and the dianion to be properly solvated, demonstrating that the rationalization used to justify the high pKa values of unconjugated bilirubin is inappropriate. Furthermore, low unconjugated bilirubin (UCB) pKa values were estimated from a linear regression analysis.

Evaluation of the Hg2+ binding potential of fulvic acids from fluorescence excitation-emission matrices.

The effect of Hg(2+) on the fluorescence intensity of three fulvic acids (Pahokee Peat, Pony Lake and Suwannee River) was studied. The fluorescence intensity decreased in the presence of added Hg(2+), while the fluorescence lifetimes were independent of the concentration of Hg(2+) in solution. These results are indicative of ground-states association between the fulvic acids and Hg(2+) with formation of stable non-fluorescent complexes (static quenching process). The analysis of the excitation-emission matrices with the Singular Value Decomposition (SVD) and Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) methods provided additional valuable information regarding the binding properties between Hg(2+) ions and specific fluorescence components of the fulvic acids. The three fulvic acids were shown to contain the same three groups of fluorophores characterized by excitation/emission pairs in the following regions: (320-330 nm/425-450 nm), (370-375 nm/465-500 nm), (290-295 nm/370-395 nm). These pairs are almost not affected by the change of pH from 2.0 to 7.0. Ryan-Weber and modified Stern-Volmer methods were used to analyze the static fluorescence quenching of the individual components. Similar conditional stability constants of Hg(2+) binding for the three components were found by both methods. The obtained log K values are in the range of 4.4 to 5.4.

Sertraline and its iodine product: experimental and theoretical vibrational studies: potential in vitro anti-thyroid activity of sertraline and iodine product toxicity with respect to male Wistar rats.

Mayor depression, obsessive-compulsive panic, social anxiety disorders are common diseases that are usually treated with sertraline hydrochloride which is the active ingredient of the well known drugs as Zoloft and Lustral. In this work, we presented a more complete vibrational characterization of the solid phase FT-IR spectra of Sertraline hydrochloride and its sertraline-iodine product in which the conformational space of the molecules was investigated performing molecular dynamic simulations within an NVT ensemble. Geometrical, electronic and vibrational properties were calculated with the density functional theory. Comparison of the simulated spectra with the experimental spectra provides important information about the ability of the computational method to describe the vibrational modes of both molecules. In addition, for the first time we present the evaluation of anti-thyroid activity of sertraline hydrochloride by using the Lang's method. Also, with the aim to evaluate the antidepressant effect of its iodine product we demonstrated for this compound the toxic effect towards the male Wistar rats.

Conformational behavior of peracetylated ß-D-mannopyranosyl methanesulfonamide: implications for the mechanism of sulfonamidoglycosylation of carbohydrate derivatives.

The conformational behavior of 2,3,4,6-tetra-O-acetyl-ß-D-mannopyranosyl methanesulfonamide has been investigated from a combined theoretical and experimental point of view. The study of the conformational space of the glycosyl sulfonamide revealed that the ß anomer is thermodynamically more stable than the α one. This fact suggests that the synthesis reaction could take place mainly under thermodynamic control as the main experimental product is the ß-anomeric form of the sulfonamide. Several intramolecular hydrogen bonds were found in the stable conformers of the N-mannopyranosyl sulfonamide under study. A relationship was found to exist between them and the relative stability of the conformers. A detailed analysis of geometrical parameters shed light into the nature of the solid state structure of the novel 2,3,4,6-tetra-O-acetyl-ß-D-mannopyranosyl methanesulfonamide in terms of exo- and endo-anomeric effects and antiperiplanar relationships. NBO calculations confirmed those findings. Calculated (1)H and (13)C NMR chemical shifts support previous findings concerning configuration and conformation assignments of the title sulfonamide. Finally, an explanation of the stereochemical outcome of sulfonamidoglycosylations, was given in terms of exo- and endo-anomeric effects and steric factors.

Photoinduced reduction of divalent mercury by quinones in the presence of formic acid under anaerobic conditions.

The laser flash photolysis technique (λ(exc)=355 nm) was used to investigate the mechanism of the HgCl(2) reduction mediated by CO(2)(-) radicals generated from quenching of the triplet states of 1,4-naphthoquinone (NQ) by formic acid. Kinetic simulations of the experimental signals support the proposed reaction mechanism. This system is of potential interest in the development of UV-A photoinduced photolytic procedures for the treatment of Hg(II) contaminated waters. The successful replacement of NQ with a commercial fulvic acid, as a model compound of dissolved organic matter, showed that the method is applicable to organic matter-containing waters without the addition of quinones.

The diatomic dication CuZn2+ in the gas phase.

In the present combined experimental and theoretical study we report the observation of the novel gas-phase dication CuZn(2+) and provide some theoretical insight into the electronic binding of this exotic metastable molecule and its formation mechanism. Using mass spectrometry we have detected four isotopomer signals of CuZn(2+) at half-integer m/z values for ion flight times of about 14 µs. CuZn(2+) was unambiguously identified by its isotopic abundance. High-current energetic Ar(+) ion bombardment of a brass surface was used for its production. Subsequent dication formation was found to take place in the ion extraction region of our mass spectrometer several tens of microns in front of the sputtered brass surface. The dication formation mechanism appears to be resonant electron transfer in soft gas-phase collisions between sputter-ejected singly charged CuZn(+) molecular ions and incoming Ar(+) projectiles. This conclusion is supported by our theoretical study that obtained an ionization energy of CuZn(+) of 15.75 eV, in excellent agreement with both the experimental and calculated ionization energy of Ar (15.76 and 15.67 eV, respectively). The ground state of CuZn(2+) is found to be a metastable one with a very shallow potential well at an internuclear equilibrium distance of about 2.7 Å the dissociation energy being very difficult to estimate. Interestingly, spin-orbit corrections are found to be necessary to get an adequate description of the metastable state of CuZn(2+), whereas relativistic corrections have no effects on neutral CuZn nor on CuZn(+).

Reduction of mercury(II) by the carbon dioxide radical anion: a theoretical and experimental investigation.

The laser flash photolysis technique (λ(exc) = 266 nm) was used to investigate the mechanism of the HgCl(2) reduction mediated by CO(2)(·-) radicals in the temperature range 291.7-308.0 K. For this purpose, the CO(2)(·-) radicals were generated by scavenging of sulfate radicals by formic acid. The absorbance of the reduced radical of methyl viologen, a competitive scavenger of CO(2)(·-), was monitored at 390 nm. Moreover, theoretical calculations, including solvent effects, were also performed within the framework of the density functional theory for various chemical species of Hg(I) and Hg(II) to aid in the modeling of the reaction of reduction of HgCl(2) by CO(2)(·-).

Observation of Zr2(2+), Cd2(2+), Hf2(2+), W2(2+), and Pt2(2+) in the gas phase.

Five homonuclear diatomic dications Zr(2)(2+), Cd(2)(2+), Hf(2)(2+), W(2)(2+), and Pt(2)(2+) have been observed in the gas phase by mass spectrometry. These exotic doubly positively charged molecules were produced indirectly in the ion extraction region of a secondary ion mass spectrometer during sputtering of zirconium, cadmium, hafnium, tungsten, and platinum metal foils, respectively, by energetic high-current Ar(+) ion surface bombardment. They were detected in positive ion mass spectra at half-integer mz values for ion flight times of the order of approximately 10(-5) s. To our knowledge, these species had not been observed before. This experimental work confirms two theoretical investigations that had predicted that W(2)(2+) and Cd(2)(2+) are long-lived metastable species in the gas phase, but contradicts two theoretical studies that had suggested that Pt(2)(2+) should be unstable with respect to fragmentation. Therefore an advanced theoretical investigation of the ground state of Pt(2)(2+) was also performed. Our calculation shows that the ground state of Pt(2)(2+) is metastable with an internuclear equilibrium distance of 2.36 A, a dissociation energy (with respect to the top of the barrier) of 2.32 eV, and an ionization potential of Pt(2)(+) of about 15.8 eV. The latter theoretical result strongly suggests that Pt(2)(2+) dication formation in our experiment may have taken place via the resonant electron transfer process Pt(2)(+) + Ar(+) --> Pt(2)(2+) + Ar.

A density-functional study on the formation of Mo(2)2+.

The presence of metastable states in the doubly ionized molybdenum dimer is studied using gradient-corrected scalar-relativistic density-functional theory. Seventeen metastable states are found within an energy range of less than 6.5 eV. All those states show lifetimes large enough to assure experimental detection. The calculation of the second adiabatic ionization potential of the neutral molybdenum dimer seems to confirm that the doubly ionized dimer is produced by the electron-capture process Mo2++Ar+-->Mo2(2+)+Ar, in which the ionization potentials of Ar and Mo2+ play a crucial role [K. Franzreb, R. C. Sobers, Jr., J. Lorincik, and P. Williams, J. Chem. Phys. 120, 7983 (2004)]. Moreover, the present results indicate that other species having ionization potentials between 13.01 and 15.34 eV could be used as projectiles to produce Mo(2)2+. It is also shown that Xe+ ions could not react with Mo2+ to produce double ionized dimers. A simple thermodynamic argument is also proposed that seems to increase the possibilities of forming Mo2(2+) from Mo2+ by using Ar+ as projectile ions.