Search

Context: The activation of C-H bonds is a fundamental process in synthetic organic chemistry, which enables their replacement by highly reactive functional groups. Coordination compounds serve as effective catalysts for this purpose, as they facilitate chemical transformations by interacting with C-H bonds. A comprehensive understanding of the mechanism of activation of this type of bond lays the foundation for the development of efficient protocols for cross-coupling reactions. We explored the activation of C(sp 2 )-H bonds in 1-Phenyl-4-vinyl-1H-1,2,3-triazole derivatives with CH 3 , OCH 3 , and NO 2 substituents in the para position of the phenyl ring, using palladium acetate as catalyst. The studied reaction is the first step for subsequent conjugation of the triazoles with naphthoquinones in a Heck-type reaction to create a C-C bond. The basic nitrogen atoms of the 1,2,3-triazole coordinate preferentially with the cationic palladium center to form an activated species. A concerted proton transfer from the terminal vinyl carbon to one of the acetate ligands with low activation energy is the main step for the C(sp 2 )-H activation. This study offers significant mechanistic insights for enhancing the effectiveness of C(sp 2 )-H activation protocols in organic synthesis., Methods: All calculations were performed using the Gaussian 09 software package and density functional theory (DFT). The structures of all reaction path components were fully optimized using the CAM-B3LYP functional with the Def2-SVP basis set. The optimized geometries were analyzed by computing the second-order Hessian matrix to confirm that the corresponding minimum or transition state was located. To account for solvent effects, the Polarizable Continuum Model of the Integral Equation Formalism (IEFPCM) with water as the solvent was used., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The metathesis reaction has been an important tool in both organic and inorganic synthetic chemistry. More specifically in polymer chemistry, ring opening metathesis polymerization (ROMP), via the formation of an active metal-carbene species (MCHR), has been widely used. The elucidation of the mechanism for ROMP opened the way for the development of well-defined catalysts, suited to local conditions. In the present study, we employed density functional theory (DFT) to investigate three reaction pathways for the formation of a species capable of activating ROMP. The active species is formed from the [RuCl 2 (PPh 3 ) 2 (pip)] complex in the presence of norbornadiene (NBD) and the carbene source ethyl diazoacetate (EDA). Formation of a hexacoordinated intermediate [RuCl 2 (PPh 3 ) 2 (pip)(NBD)] is favored in the first step, with NBD doubly coordinated to the [RuCl 2 (PPh 3 ) 2 (pip)] moiety. Analysis of donation (X → Ru) and back-donation (Ru → X) processes in the [RuCl 2 (PPh 3 ) 2 (pip)(NBD)] complex shows that piperidine behaves as a σ donor, while NBD behaves as a π donor and the PPh 3 groups act as π acceptors. The intensity of the orbital component is predominant in relation to the steric component in the complex. Thus, we propose that the reaction occurs through the formation of a hexacoordinated complex, followed by the dissociation of a PPh 3 group, thus forming a complex where NBD is doubly coordinated to the metal center. Coordination of EDA leads finally to the catalyst capable of forming the metallocyclobutane intermediate required for the ROMP reaction.

Context: A complex supramolecular process involving electrostatic and dispersion interactions and asphaltene aggregation is associated with detrimental petroleum deposition and scaling that pose challenges to petroleum recovery, transportation, and upgrading. The homodimers of seven heterocyclic model compounds, representative of moieties commonly found in asphaltene structures, were studied: pyridine, thiophene, furan, isoquinoline, pyrazine, thiazole, and 1,3-oxazole. The contributions of hydrogen bonding involving water bridges spanning between dimers and π-π stacking to the total interaction energy were calculated and analyzed. The distance between the planes of the aromatic rings is correlated with the π-π stacking interaction strength. All the dimerization reactions were exothermic, although not spontaneous. This was mostly modulated by the strength of the hydrogen bond of the water bridge and the π-π stacking interaction. Dimers bridged by two water molecules were more stable than those with additional water molecules or without any water molecule in the bridge. Energy decomposition analysis showed that the electrostatic and polarization components were the main stabilizing terms for the hydrogen bond interaction in the bridge, contributing at least 80% of the interaction energy in all dimers. The non-covalent interaction analysis confirmed the molecular sites that had the strongest (hydrogen bond) and weak (π-π stacking) attractive interactions. They were concentrated in the water bridge and in the plane between the aromatic rings, respectively., Methods: The density functional ωB97X-D with a dispersion correction and the Def2-SVP basis set were employed to investigate supramolecular aggregates incorporating heterocycles dimers with 0, 1, 2, and 3 water molecules forming a stabilizing bridge connecting the monomers. The non-covalent interactions were analyzed using the NCIplot software and plotted as isosurface maps using Visual Molecular Dynamics., (© 2024. Crown.)

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established S N 1 and S N 2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride ( i PrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number ( n = 1, 3, 5, 7, 9, and 12) and configurations of H 2 O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of i PrCl follows a loose-S N 2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of Δ H ‡ ≈ 21 kcal mol -1 , with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an S N 1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Recently, structural elucidation of natural products has undergone a revolution. The combined use of different modern spectroscopic methods has allowed obtaining a complete structural assignment of natural products using small amounts of sample. However, despite the extraordinary ongoing advances in spectroscopy, the mischaracterization of natural products has been and remains a recurrent problem, especially when the substance presents several stereogenic centers. The misinterpretation of nuclear magnetic resonance (NMR) data has resulted in frequent reports addressing structural reassignment. In this context, a great effort has been devoted to developing quantum chemical calculations that simulate NMR parameters accurately, allowing to achieve a more precise spectral interpretation. In this work, we employed a protocol for theoretical calculations of 1 H NMR chemical shifts and coupling constants using density functional theory (DFT), followed by the application of the DP4+ method to revisit the structure of Heliannuol L, a member of the Heliannuol class, isolated from Helianthus annuus. Our results indicate that the originally proposed structure of Heliannuol L needs a stereochemical reassignment, placing the hydroxyl bonded to C10 in the opposite side of the methyl and hydroxyl groups bonded to C7 and C8, respectively., (© 2021 John Wiley & Sons, Ltd.)

To investigate the herbicidal potential of 2,5-diketopiperazines (2,5-DKPs), we applied a known protocol to produce a series of 2,5-DKPs through intramolecular N -alkylation of Ugi adducts. However, the method was not successful for the cyclization of adducts presenting aromatic rings with some substituents at the ortho position. Results from DFT calculations showed that the presence of voluminous groups at the ortho position of a benzene ring results in destabilization of the transition structure. Lower activation enthalpies for the S N 2-type cyclization of Ugi adducts were obtained when bromine, instead of a chlorine anion, is the leaving group, indicating that the activation enthalpy for the cyclization step controls the formation of the 2,5-DKP. Some Ugi adducts and 2,5-DKPs formed crystals with suitable qualities for single-crystal X-ray diffraction data collection. Phytotoxic damage of some 2,5-DKPs on leaves of the weed Euphorbia heterophylla did not differ from those caused by the commercial herbicide diquat.

We synthesized ten enamine naphthoquinones with yields ranging from 43 to 76%. These compounds were screened for their in vitro antiproliferative activities by MTT assay against four types of human cancer cell lines: HCT116, PC3, HL60 and SNB19. The naphthoquinones bearing the picolylamine (7) and quinoline (12) moieties were the most actives (IC 50  < 24 μM for all the cell lines), which were comparable or better to the values obtained for the control drugs. In silico evaluations allowed us to develop a qualitative Structure-Activity Relationship which suggest that electrostatic features, particularly the C 2 -C 3 internuclear repulsion and the molecular dipole moment, relate to the biological response. Furthermore, Molecular Docking simulations indicate that the synthetic compounds have the potential to act as anticancer molecules by inhibiting topoisomerase-II and thymidylate synthase., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Herbicides are agrochemicals applied in the control of weeds. With the frequent and repetitive use of these substances, serious problems have been reported. Compounds of natural origin and their derivatives are attractive options to obtain new compounds with herbicidal properties. By aiming to develop compounds with potentiated herbicidal activity, phenoxyacetic acids were synthesized from eugenol and guaiacol. The synthesized compounds were characterized and the herbicidal potential of phenoxyacetic acids and precursors was evaluated through bioassays regarding the germination and initial development of Lactuca sativa and Sorghum bicolor seedlings, with the induction of DNA damage. The induction of changes in the mitotic cycle of meristematic cells of roots of L. sativa was also analyzed. At the concentration of 3 mmol L-1, phenols and their respective phenoxyacetic acids presented phytotoxic and cytotoxic activities in L. sativa and S. bicolor. Eugenol and guaiacol also presented genotoxic action in L. sativa. The toxic effect of eugenoxyacetic acid was more pronounced in L. sativa than in S. bicolor, similar to the commercial 2,4-D herbicide. Molecular properties of the phenols and their derivatives phenoxyacetic acids were compared with the ones obtained for the herbicide 2,4-D, where it was found a correlation between their molecular properties and bioactivity.

Prostate cancer is an important cause of death in the male population and for which there is no satisfactory chemotherapy. Herein a new series of chalcone hybrids containing 2H-1,2,3-triazole core as the ring B has been synthesized and evaluated in vitro against PC-3 prostate cancer cell line. Compounds 4a, 4c and 4e significantly reduced cell viability and showed IC 50 of 28.55, 15.64 and 25.56 µM, respectively. The structure-activity relationship supported by computational chemistry points that the polarity of the molecular surface area should have some relevance to the efficiency of the compounds, in particular the ratio of the partial positive charge sites and the total molecular surface area exposed to the cell environment., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The regioselective formation of α- and β-lapachone via hetero-Diels-Alder reactions was investigated by experimental and computational approaches. The experimentally observed α-selectivity was explored in detail, revealing that the lower energy barrier for the formation of α-lapachone is a result of lower Pauli repulsion throughout the reaction path, when compared to the β-isomer. By comparing equivalent points on both α- and β-lapachone potential energy surfaces (PES), according to the activation strain model (ASM) and energy decomposition analysis (EDA), we were able to demonstrate that the Pauli repulsion term increases more significantly when going from reactants to TS β than to TS α , resulting in lower interaction energy in the early stages of the reaction path and in a later transition state for β-lapachone. Moreover, we confirmed that regio- and diastereoselectivity trends previously reported for other quinone methide intermediates are also observed for 3-methylene-1,2,4-naphthotriones, such as small endo / exo diastereoselectivity, as well as pronounced ortho / meta regioselectivity for reactions performed with dienophile containing electron-releasing groups. The results presented here provide a deeper understanding of the reactivity of quinone methide derivatives, aiding the future rational design of the reaction condition, structural modification of possible quinone methide intermediates, and the development of more selective synthetic routes for quinone derivatives.

1,3-Dipolar cycloaddition (1,3-DC) reactions are powerful synthetic tool to obtain highly functionalized 5-membered heterocycles, starting from a 1,3-dipole and a dipolarophile in a single step. The reactivity of these systems is usually rationalized in terms of Frontier Molecular Orbital Theory (FMOT), which neglects a possible contribution of an open-shell weakly coupled singlet-diradical specie. In this work, the broken-symmetry approach is used to estimate the singlet-diradical character of 18 dipoles of the second period of the periodic table, classified as allyl-type N-centered, allyl-type O-centered, and propargyl-type 1,3-dipoles, providing a rationalization for 1,3-DC reactivity. The intramolecular cyclization of bent allyl-type N- and O-centered dipoles into 3-membered rings was also analyzed, and revealed that the energetic change is associated with the spin densities of peripheral atoms. Finally, a close relationship between the energy for the ring-opening process of the cyclic configuration and the reactivity of 1,3-dipoles toward 1,3-dipolar cycloaddition reaction was also found. Graphical abstract.

4-Oxoquinolines are a class of organic substances of great importance in medicinal chemistry, due to their biological and synthetic versatility. N -1-Alkylated-4-oxoquinoline derivatives have been associated with different pharmacological activities such as antibacterial and antiviral. The presence of a carboxamide unit connected to carbon C-3 of the 4-oxoquinoline core has been associated with various biological activities. Experimentally, the N-ethylation reaction of N -benzyl-4-oxo-1,4-dihydroquinoline-3-carboxamide occurs at the nitrogen of the oxoquinoline group, in a regiosselective way. In this work, we employed DFT methods to investigate the regiosselective ethylation reaction of N -benzyl-4-oxo-1,4-dihydroquinoline-3-carboxamide, evaluating its acid/base behavior and possible reaction paths.

Semisynthetic phenol derivatives were obtained from the natural phenols: thymol, carvacrol, eugenol, and guaiacol through catalytic oxychlorination, Williamson synthesis, and aromatic Claisen rearrangement. The compounds characterization was carried out by 1 H NMR, 13 C NMR, and mass spectrometry. The natural phenols and their semisynthetic derivatives were tested for their antimicrobial activity against the bacteria: Staphylococcus aureus, Escherichia coli, Listeria innocua, Pseudomonas aeruginosa, Salmonella enterica Typhimurium, Salmonella enterica ssp. enterica, and Bacillus cereus. Minimum inhibitory concentration (MIC) and minimal bactericidal concentration (MBC) values were determined using concentrations from 220 to 3.44 μg mL -1 . Most of the tested compounds presented MIC values ≤220 μg mL -1 for all the bacteria used in the assays. The molecular properties of the compounds were computed with the PM6 method. Through principle components analysis, the natural phenols and their semisynthetic derivatives with higher antimicrobial potential were grouped.

A series of B3LYP/6-311+G(d,p) calculations of the affinity of monodentate ligands for [Cd(H 2 O) 3 ] 2+ are performed. Three types of ligands containing O (phosphine oxide, lactam, amide, carboxylic acid, ester, ketone, aldehyde, ether, halohydrin, enol, furan), N (thiocyanate, amine, ammonia, azide), and S (thioester, thioketone, thiol, thiophene, disulfide) interacting atoms are investigated. The results show that phosphine oxide has the largest affinity for the cadmium cation due to the polarization of the P=O bond. As the P atom has a large atomic radius, the O atom can polarize the electronic cloud enhancing its amount of electronic charge and favoring the interaction with Cd 2+ . The affinity order found is phosphine oxide > thioester > lactam > amide > carboxylic acid > ester > thioketone > ketone > thiocyanate > amine > ammonia > aldehyde > ether > thiol > thiophene > enol > halohydrin > disulfide > azide > furan ligands. These results were also corroborated by the functional M06-2X. The electronic effects (resonance and induction) of neighboring groups of the interacting atom modulate the strength of metal-ligand binding. For almost all the O-donor ligands the electrostatic component has the same magnitude as the covalent term, while for the N- and S-donor ligands the covalent term is predominant. The polarization term accounts for twice the exchange term as part of the covalent component. The dispersion term varies less than 2 kcal mol -1 for the complexes analyzed. The Pauli repulsion term is correlated with the metal ligand distance, increasing in the compounds with decreased metal-ligand bond length. The charge between the interacting atoms is also strongly correlated with both the interacting strength and the electrostatic interaction component. The natural bond orbital analysis highlights correlations of the bond order, and S and P contributions of the interacting metal-ligand orbital with the coordination strength. Graphical abstract The affinity of 20 monodentate ligands with different functional groups for the [Cd(H 2 O) 3 ] 2+ cation is calculated based on the interaction enthalpy and Gibbs free energy for the substitution of one water molecule from the fully hydrated cation. The affinity is correlated with geometric, electronic, and energetic parameters of the ligands and the complexes as well as with energy decomposition and natural bond order analyses results.