Search Results (27)

The objective of this study was to use Density Functional Theory (DFT) calculations to examine how boron doping modulates the electronic properties of graphene quantum dots (GQDs) and their interaction with the Hg²⁺ ion. Boron doping decreases the HOMO-LUMO gap and increases the GQD’s electrophilic character, facilitating charge transfer to the metal ion. The adsorption energy results were negative, indicating electronic stabilization of the combined systems, without implying thermodynamic favorability, with the GQD@3B_Hg²⁺ system being the strongest at −349.52 kcal/mol. The analysis of global parameters (chemical descriptors) and the study of non-covalent interactions (NCIs) supported the affinity of Hg²⁺ for doped surfaces, showing that the presence of a single boron atom contributes to clear attractive interactions. In general, configurations doped with 1 or 2 boron atoms exhibit satisfactory performance, demonstrating that boron doping effectively modulates the reactivity and adsorption properties of GQD for efficient Hg²⁺ capture. Full article

A thiazole–thiophene derivative, (E)-4-(2-(2-(1-(5-chlorothiophen-2-yl)ethylidene)hydrazinyl)thiazol-4-yl)benzonitrile (CTHTBN), was synthesized via a one-pot multicomponent reaction involving 5-chloro-2-acetylthiophene, thiosemicarbazide, and 4-(2-bromoacetyl)benzonitrile. The synthesized compound was characterized by FT-IR, ¹H NMR, and ¹³C NMR spectroscopy, confirming the formation of the title compound. Density Functional Theory (DFT) calculations at the B3LYP/6-311G(d,p) level were performed to explore the electronic structure and reactivity of CTHTBN. The HOMO and LUMO energies were found to be −5.75 eV and −2.03 eV, respectively, with an energy gap (E_g) of 3.72 eV, suggesting a balanced chemical stability and reactivity. The dipole moment of 7.9381 Debye indicated substantial polarity, favorable for biological interactions. Global reactivity descriptors, including chemical hardness (η = 1.86 eV), chemical softness (σ = 0.5376 eV⁻¹), electronegativity (χ = 3.89 eV), electrophilicity index (ω = 4.07 eV), and maximum charge transfer capacity (ΔN_max = 2.09), further supported the molecule’s electronic competence. Molecular docking against M. tuberculosis CYP51 revealed a strong binding affinity (−8.8 kcal/mol), stabilized by π–sulfur contacts with MET79 and PHE83, π–π stacking with TYR76, and π–π T-shaped interactions with PHE83 and the heme cofactor. Additional π–alkyl interactions with LEU321, ALA325, and the heme group reinforced hydrophobic complementarity, confirming efficient accommodation of CTHTBN in the active site. These findings suggest that CTHTBN holds promising potential as an antimycobacterial agent targeting CYP51 and may be explored in future biological studies. Full article

A comprehensive analysis of key findings derived from density functional theory (DFT) studies reveals that current theoretical data on curcumin remain incomplete, underscoring the need for further computational investigation to achieve a more thorough understanding of its chemical and biological reactivity. This study addresses these gaps through four primary objectives: (i) determination of a complete set of thermodynamic descriptors and elucidation of the multi-step anti-radical mechanisms of the neutral, radical, anionic, and radical–anionic forms of curcumin; (ii) calculation of global chemical reactivity descriptors of curcumin in various solvent environments; (iii) theoretical reproduction of experimentally determined pK_a values for all active sites within the molecule; and (iv) examination of the effects of dispersion interactions and solvent polarity on the reactivity descriptors of keto–enol forms of curcumin. The results obtained provide enhanced insight into the molecular behavior of curcumin, facilitating improved predictions of its reactivity under diverse conditions. Moreover, the findings indicate a potential structural modification of the keto form of curcumin, involving the attachment of two 4-hydroxy-3-methoxyphenyl-prop-1-en-2-one moieties to the methylene group. The resulting modeled compound, referred to as di-curcumin, exhibits enhanced chemical reactivity and increased anti-radical potential. Full article

This study investigates the structural and energetic properties of hydrogen-bonded complexes between indole and a range of aliphatic, cyclic, and aromatic ketones using a combined vibrational spectroscopic and quantum-chemical approach. FTIR measurements in CCl₄ revealed redshifts in the N-H stretching vibration of indole upon complexation, with formation constants (K_a) ranging from 0.3 to 6.6 M⁻¹. Cyclohexanone displayed the strongest binding, while benzophenone exhibited the weakest interaction. Quantum-chemical calculations, employing CREST and MMFF94 conformational sampling, along with M06-2X/6-311++G(d,p) optimizations, confirmed the formation of hydrogen bonds and additional weak interactions that govern the stability of the complex. QTAIM analysis revealed moderate closed-shell hydrogen bonds with electron densities at the bond critical points (ρ) ranging from 0.010 to 0.019 a.u. and potential energy densities (V) from −18.4 to −36.4 kJ mol⁻¹. Multivariate regression analysis established strong correlations (R² = 0.928 and 0.957) between experimental binding constants and theoretical descriptors, including binding energy, NBO charge on oxygen atom, ionization potential, and electrophilicity index, highlighting the interplay between geometric, electronic, and global reactivity factors. This comprehensive study underlines the predictive power of spectroscopic and quantum descriptors for assessing hydrogen bonding in biologically relevant systems. Full article

Peptoids are peptidomimetics in which the side chain is attached to the nitrogen of the amide group rather than the α-carbon. This alteration in the backbone structure is highly valued because it endows beneficial properties, including enhanced resistance to proteolysis, greater immunogenicity, improved biostability, and superior bioavailability. In this current study, we focused on the Ugi-4CR-based one-pot synthesis of peptoids using 1,4-dithiane-2,5-diol as the carbonyl component together with amine, carboxylic acid, and isocyanides. Four new peptoids—5a, 5b, 5c, and 5d—were designed and efficiently prepared in good chemical yields and were subjected to DFT investigations for their electronic behavior. These compounds have free OH, SH, and terminal triple bonds for further chemistry. In a computational analysis, the spectral data of compounds 5a–5d were juxtaposed with calculated spectral values derived from the B3LYP/6-311G(d,p) level. The electronic excitation and orbital contributions of 5a–5d were predicted using TD-DFT calculations. A natural bond order (NBO) analysis was utilized to investigate the electronic transition of newly synthesized peptoids, focusing on their charge distribution patterns. Furthermore, MEP and NPA analyses were conducted to predict charge distribution in these compounds. The reactivity and stability of the targeted peptoids were evaluated by global reactivity descriptors, which were determined with frontier molecular orbital analysis. The DFT results revealed that compound 5c displayed marginally higher reactivity compared to 5a, 5b, and 5d, possibly due to its extended conjugation. Full article

Kapakahines A–G are natural products isolated from the marine sponge Carteriospongia sp., characterized by complex molecular architectures composed of fused rings and diverse functional groups. Preliminary studies have indicated that some of these peptides may exhibit cytotoxic and antitumor activities, which has prompted interest in further exploring their chemical and pharmacokinetic properties. Computational chemistry—particularly Conceptual Density Functional Theory (CDFT)-based Computational Peptidology (CP)—offers a valuable framework for investigating such compounds. In this study, the CDFT-CP approach is applied to analyze the structural and electronic properties of Kapakahines A–G. Alongside the calculation of global and local reactivity descriptors, predicted ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiles and pharmacokinetic parameters, including pKa and LogP, are evaluated. The integrated computational analysis provides insights into the stability, reactivity, and potential drug-like behavior of these marine-derived cyclopeptides and contributes to the theoretical groundwork for future studies aimed at optimizing their bioactivity and safety profiles. Full article

Graphene oxide (GO) is considered as a promising adsorbent material for the removal of metal from aqueous environments. Here, we have used the density functional theory (DFT) approach and a combination of parameters to characterise the interactions of GO with lead (Pb) and cadmium (Cd), i.e., typical harmful metals often found in water. Our model systems consist of a singly and doubly adsorbed neutral (${\mathrm{Pb}}^0$, ${\mathrm{Cd}}^0$) and charged (${\mathrm{Pb}}^{2+}$, ${\mathrm{Cd}}^{2+}$) atoms adsorbed on the GO nanoparticle of the chemical formula ${\mathrm{C}}_{30}$${\mathrm{H}}_{14}$${\mathrm{O}}_{15}$. We show that a single charged metal ion binds more strongly than a neutral atom of the same type. Moreover, to determine the possibility of multiple adsorptions of the GO nanoparticle, two metal atoms of the same species were co-adsorbed on its surface. We found a site-dependent adsorption energy such that when two atoms of the same specie are adsorbed at sites ${\mathrm{S}}_i$ and ${\mathrm{S}}_j$, the binding energy per atom depends on whether one of the two atoms is adsorbed firstly on the ${\mathrm{S}}_i$ or ${\mathrm{S}}_j$ sites. Furthermore, the binding energy per atom for the two co-adsorbed atoms of the same specie (i.e., neutral or charged) is less than the binding energy of a singly adsorbed atom. This suggests that atoms may become less likely to be adsorbed on the GO nanoparticle when their concentration increases. We adduce the origin of this observation to be interplay between the metal–metal interaction on the one hand and GO–metal on the other, with the former resulting in less binding for the charged adsorbed metals in particular, due to repulsive interaction between two positively charged ions. The frontier molecular orbitals analysis and the calculated global reactivity descriptors of the respective GO–metal complexes revealed that all the GO–metal complexes have a smaller HOMO–LUMO gap (HLG) relative to that of pristine metal-free GO nanoparticle. This may indicate that although the GO–metal complexes are stable, they are less stable compared to metal-free GO nanoparticles. The negative values of the chemical potentials obtained for all the GO–metal complexes further confirm their stability. Our work differs from previous experimental studies in that those lacked details of the interaction mechanisms between GO, Pb and Cd, as well as previous theoretical studies which used limited numbers of parameters to characterise the GO–metal interactions. Rather, we present a set of parameters or descriptors which provide comprehensive physical and electronic characterisation of GO–metal systems as obtained via the DFT calculations. These parameters, along with those reported in previous studies, may find applications in rational design and high-throughput screening of graphene-based materials for water purification, as an example. Full article

Nowadays, the effective processing of natural monoterpenes that constitute renewable biomass found in post-production waste into products that are starting materials for the synthesis of valuable compounds is a way to ensure independence from non-renewable fossil fuels and can contribute to reducing global carbon dioxide emissions. The presented research aims to determine, based on DFT calculations, the activity and reactivity of limonene, an organic substrate used in previous preparative analyses, in comparison to selected monoterpenes such as cymene, pinene, thymol, and menthol. The influence of the solvent model was also checked, and the bonds most susceptible to reaction were determined in the examined compounds. With regard to E_HOMO, it was found that limonene reacts more easily than cymene or menthol but with more difficultly than thymol and pienene. The analysis of the global chemical reactivity descriptors “locates” the reactivity of limonene in the middle of the studied monoterpenes. It was observed that, among the tested compounds, the most reactive compound is thymol, while the least reactive is menthol. The demonstrated results can be a reference point for experimental work carried out using the discussed compounds, to focus research on those with the highest reactivity. Full article

On the basis of density functional theory (DFT) at the B3LYP/cc-pVQZ level with the C-PCM solvation model, a comparative analysis of the reactivity of the garlic metabolites 2-propenesulfenic acid (PSA) and allyl mercaptan (AM, 2-propene-1-thiol) was performed. In particular, the thermodynamic descriptors (BDE, PA, ETE, AIP, PDE, and G_acidity) and global descriptors of chemical activity (ionization potential (IP), electron affinity (EA), chemical potential (μ), absolute electronegativity (χ), molecular hardness (η) and softness (S), electrophilicity index (ω), electro-donating (ω⁻) and electro-accepting (ω⁺) powers, and Ra and Rd indexes) were determined. The calculations revealed that PSA is more reactive than AM, but the latter may play a crucial role in the deactivation of free radicals due to its greater chemical stability and longer lifetime. The presence of a double bond in AM enables its polymerization, preserving the antiradical activity of the S-H group. This activity can be amplified by aryl-substituent-containing hydroxyl groups. The results of the calculations for the simplest phenol–AM derivative indicate that both the O-H and S-H moieties show greater antiradical activity in a vacuum and aqueous medium than the parent molecules. The results obtained prove that AM and its derivatives can be used not only as flavoring food additives but also as potent radical scavengers, protecting food, supplements, cosmetics, and drug ingredients from physicochemical decomposition caused by exogenous radicals. Full article

The replacement of carbon with a heteroatom within the structure of a fullerene gives the possibility of obtaining compounds with adjustable properties. The influence of aza-substitution on C₂₄ fullerenes was investigated and a comparison of HF and DFT calculations was performed. Various substitution patterns were proposed and the characterization of C₂₂N₂ and C₂₀N₄ structures was performed. Global reactivity descriptors like chemical potential, hardness, HOMO–LUMO gap and singlet–triplet gap were computed. Aromaticity descriptors like delocalization indices and NICS(0) index were employed for the characterization of each six-membered ring of the studied fullerenes. The possible use of aza-fullerenes as drug delivery systems for two adamantane-derived antivirals was evaluated through molecular docking studies. The best results were obtained for the fullerenes with a pronounced hydrophobic character, the favored configuration of the antiviral drugs being the one oriented toward the side consisting of carbon atoms of the fullerenes. Full article

Molecules sourced from marine environments hold immense promise for the development of novel therapeutic drugs, owing to their distinctive chemical compositions and valuable medicinal attributes. Notably, Talarolide A and Talaropeptides A–D have gained recent attention as potential candidates for pharmaceutical applications. This study aims to explore the chemical reactivity of Talarolide A and Talaropeptides A–D through the application of molecular modeling and computational chemistry techniques, specifically employing Conceptual Density Functional Theory (CDFT). By investigating their chemical behaviors, the study seeks to contribute to the understanding of the potential pharmacological uses of these marine-derived compounds. The molecular geometry optimizations and frequency calculations were conducted using the Density Functional Tight Binding (DFTBA) method. This was followed by a subsequent round of geometry optimization, frequency analysis, and computation of electronic properties and chemical reactivity descriptors. We employed the MN12SX/Def2TZVP/H2O model chemistry, utilizing the Gaussian 16 program and the SMD solvation model. The analysis of the global reactivity descriptors arising from CDFT was achieved as well as the graphical comparison of the dual descriptor DD revealing the areas of the molecules with more propensity to suffer a nucleophilic or electrophilic attack. Additionally, Molinspiration and SwissTargetPrediction were considered for the calculation of molecular characteristics and predicted biological targets. These include enzymes, nuclear receptors, kinase inhibitors, GPCR ligands, and ion channel modulators. The graphical results show that Talarolide A and the Talaropeptides A–D are likely to behave as protease inhibitors. Full article

The corrosion of materials remains a critical challenge with significant economic and infrastructural impacts. A comprehensive understanding of adsorption characteristics of phytochemicals can facilitate the effective design of high-performing environmentally friendly inhibitors. This study conducted a computational exploration of hydroxytyrosol (HTR) and tyrosol (TRS) (potent phenolic compounds found in olive leaf extracts), focusing on their adsorption and reactivity on iron surfaces. Utilizing self-consistent-charge density-functional tight-binding (SCC-DFTB) simulations, molecular dynamics (MD) simulations, and quantum chemical calculations (QCCs), we investigated the molecules’ structural and electronic attributes and interactions with iron surfaces. The SCC-DFTB results highlighted that HTR and TRS coordinated with iron atoms when adsorbed individually, but only HTR maintained bonding when adsorbed alongside TRS. At their individual adsorption, HTR and TRS had interaction energies of −1.874 and −1.598 eV, which became more negative when put together (−1.976 eV). The MD simulations revealed parallel adsorption under aqueous and vacuum conditions, with HTR demonstrating higher adsorption energy. The analysis of quantum chemical parameters, including global and local reactivity descriptors, offered crucial insights into molecular reactivity, stability, and interaction-prone atomic sites. QCCs revealed that the fraction of transferred electron ∆N aligned with SCC-DFTB results, while other parameters of purely isolated molecules failed to predict the same. These findings pave the way for potential advancements in anticorrosion strategies leveraging phenolic compounds. Full article

This study presents a comprehensive exploration of the structure–reactivity relationship of (E)-3-bromo-4-((4-((1-(4-chlorophenyl)ethylidene)amino)-5-phenyl-4H-1,2,4-triazol-3-yl)thio)-5-((2-isopropylcyclohexyl)oxy)furan-2(5H)-one. The study embarked on an in-depth investigation into the solid-state crystal structure of this organic compound, employing computational Density Functional Theory (DFT) and related methodologies, which have not extensively been used in the examination of such compounds. A single-crystal X-ray diffraction (SCXRD) analysis was initially performed, supplemented by a Hirshfeld surfaces analysis. This latter approach was instrumental in visualizing and quantifying intermolecular interactions within the crystal structures, offering a detailed representation of the molecule’s shape and properties within its crystalline environment. The concept of energy framework calculations was utilized to understand the varied types of energies contributing to the supramolecular architecture of the molecules within the crystal. The Conceptual DFT (CDFT) was applied to predict global reactivity descriptors and local nucleophilic/electrophilic Parr functions, providing a deeper understanding of the compound’s chemical reactivity properties. The aromatic character and π–π stacking ability were also evaluated with the help of LOLIPOP and ring aromaticity measures. This comprehensive approach not only provides a detailed description of the structure and properties of the investigated compound but also offers valuable insights into the design and development of new materials involving 1,2,4-triazole systems. Full article

We report the time-efficient synthesis of quinolin-8-yl 4-chlorobenzoate (3) via an O-acylation reaction between 8-hydroxyquinoline (1) and 4-chlorobenzoyl chloride (2) mediated by triethylamine in acetonitrile under heating at 80 °C for 20 min in the Monowave 50 reactor. This protocol is distinguished by its short reaction time, operational simplicity, and clean reaction profile. The structure of 3 was fully characterized through a combination of analytical techniques, including NMR, IR, and UV–Vis spectroscopy, MS spectrometry, differential scanning calorimetry (DSC), thermogravimetry (TG), and crystallographic studies. Interestingly, X-ray diffraction analyses of 3 show that the crystal structure is characterized by C-H···N, C-H···O, Cl···π, and π···π interactions. The molecular conformation presents an orthogonal orientation between aromatic rings in the solid state. The calculated interaction energies using the CE-B3LYP model show that dispersion forces act in a higher proportion to build the crystal, which is consistent with the few short hydrogen interactions detected. Electrostatic potential maps suggest the formation of σ-holes over the Cl atoms. Although they can behave as both Lewis acid and base sites, Cl··Cl interactions are absent due to the shallow depth of these σ-holes. Quantum chemical descriptors and global reactivity descriptors were examined using the B3LYP method with the 6-31G(d,p) basis set implemented in CrystalExplorer. Finally, compound 3 exhibited low activity against HOP-92 and EKVX non-Small-cell lung and UO-31 Renal cancer cell lines, with a growth inhibition percentage (GI%) ranging from 6.2% to 18.1%. Full article

A convenient and efficient synthetic protocol for the new selenadiazole. Thiadiazole and diazaphosphole derivatives incorporating a pyridazine moiety originating from 4-(4-aminophenyl)-4-oxobutanoic acid (1) were described. All newly synthesized compounds were evaluated for their antimicrobial activity using the disk diffusion method, and their cytotoxicity was evaluated against brine shrimp lethality bioassay. Using density functional theory (DFT), the frontier molecular orbital (FMO) and molecular electrostatic potential (MEPS) were studied to estimate the chemical reactivity and kinetic stability of each structure. Therefore, global descriptor parameters like electronegativity (χ), chemical hardness (η), and global softness (σ) were calculated. Consequently, the attained results were compared with the experimental data of the biological activity of the studied structures. Full article