Search Results (22)

A comparative study was carried out using density functional theory of the adsorption of phenol and p-chlorophenol on two molecular models of biopolymers in aqueous medium: a chitosan dimer and cellobiose. Twelve adsorbent–adsorbate complexes with three initial orientations per system were optimized, and their structural, electronic, and non-covalent properties were analyzed using boundary orbitals, molecular electrostatic potential, NCI/RDG, and QTAIM. In all four systems, the most stable geometry corresponded to the anchoring of the contaminant hydroxyl group to an adsorbent hydroxyl group, identifying O–H···O as the guiding motif of molecular recognition. However, conformational selectivity was strongly dependent on the adsorbent and the aromatic substituent. For phenol, the alternative orientations were 2.7 and 21.2 kcal mol⁻¹ in chitosan and 6.6 and 48.9 kcal mol⁻¹ in cellobiose. For p-chlorophenol, chitosan showed a much more severe discrimination, with penalties of 43.6 and 46.44 kcal mol⁻¹. In contrast, in cellobiose, the alternative orientations remained close to the minimum, with differences of 5.1 and 3.5 kcal mol⁻¹. The effect of Cl was also reflected in the electron topology: PC increased from 3.2 × 10⁻² to 6.34 × 10⁻² a.u. in chitosan and from 3.2 × 10⁻² to 4.2 × 10⁻² a.u. in cellobiose, while |V|/G went from 3.6 to 7.5 in chitosan and from 3.00 to 3.1 in cellobiose. Overall, the results show that p-chlorophenol interacts more intensely and selectively with chitosan, whereas cellobiose favors a more flexible, less topologically differentiated adsorption. These results clarify how a para-chloro substituent reorganizes hydrogen-bond-driven adsorption on two biopolymer microenvironments with different functional heterogeneity. Full article

Water pollution from phenols remains a critical concern due to their persistence, toxicity, and industrial prevalence. Graphene oxide (GOx), with its functional groups and large surface area, offers strong adsorption potential. Using density functional theory (DFT), reduced density gradient (RDG), and quantitative structure–activity relationship (QSAR), we examined how protonation and substituents influence phenol adsorption. Deprotonated phenolates bind more strongly to GO than neutral species via electrostatics and H-bonding. Substituents alter affinity: halogens enhance it, bulky alkyls hinder it, and nitro groups show electron-withdrawing effects. Bisphenolate A displayed multidentate binding. QSAR models reproduced DFT energies with R² > 0.99, enabling fast prediction. These results highlight how pH speciation and substituents govern adsorption on GO, guiding the design of efficient water treatment materials. Full article

Background: Rapidly growing mycobacteria (RGM) are microorganisms with variable pathogenicity, which can cause different clinical forms of mycobacterioses. They can form structured communities at the liquid-air interface and adhere to animate and inanimate solid surfaces, characterizing one of their most powerful mechanisms of resistance and survival, named biofilms. Objectives: Here, a novel series of sulfamethoxazole (SMTZ) Schiff bases were obtained by the condensation of the primary amine from SMTZ core with six different aldehydes to evaluate their antimicrobial and antibiofilm activities, as well as physicochemical and in silico characteristics. Methods: The compounds L1–L6 included: pyridoxal hydrochloride (L1), salicylaldehyde (L2), 3-methoxysalicylaldehyde (L3), 2-hydroxy-1-naphthaldehyde (L4), 3-allylsalicylaldehyde (L5), and 4-(diethylamino)salicylaldehyde (L6). MIC determination was performed against standard strains and seven clinical isolates. Time-kill assays, biofilm inhibition assays, atomic force microscopy, and peripheral blood mononuclear cell cytotoxicity assays were carried out. Density functional theory (DFT) calculations using quantum descriptors, Mulliken charges, Fukui functions, non-covalent interactions (NCI), and reduced density gradient (RDG), along with molecular docking calculations to DHS, LasR, and PqsR, supported the experimental trend. Results: The compounds L1–L6 showed a significant capacity to inhibit the growth of RGM, with MIC values in the range of 0.61 to 1.22 μg mL⁻¹, which are significantly lower than those observed for the parent compound SMTZ, demonstrating superior antimicrobial potency. To deepen antimicrobial activity assays, L1 was chosen for further evaluations and showed a significant ability to inhibit the growth of RGM in both planktonic and biofilm forms. In addition, atomic force microscopy views great changes in topography, electrical force, and nanomechanical properties of microorganisms. The cytotoxic assays with the peripheral blood mononuclear cell model suggest that the new compound may be considered as an antimicrobial alternative, as well as a safe substance showing selectivity indexes in the range of efficacy. Conclusions: Density functional theory (DFT) calculations were performed to obtain quantum descriptors, Mulliken charges, Fukui functions, non-covalent interactions (NCI), and reduced density gradient (RDG), which, with molecular docking calculations to DHS, LasR, and PqsR, supported the experimental trend. Full article

This study employs density functional theory (DFT) and time-dependent DFT (TD-DFT) to systematically investigate the ground- and excited-state properties of hybrid systems composed of CdSe quantum dots (QDs) with graphene and boron nitride (BN). Through Multiwfn wavefunction analysis, we calculated the highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) gaps and density of states (DOS), revealing distinct symmetry-dependent electronic characteristics. The HOMO–LUMO gap analysis demonstrates graphene’s superior charge transfer capability compared to BN, attributed to its higher structural symmetry enabling more efficient orbital overlap. DOS analysis further confirms the enhanced electrical conductivity in symmetry-matched graphene hybrids. The independent gradient model (IGM) and reduced density gradient (RDG) analyses reveal fundamentally different interfacial interaction patterns: the graphene hybrid exhibits uniform van der Waals interactions, consistent with its hexagonal symmetry, while the BN system shows heterogeneous interactions with localized hydrogen bonding due to symmetry reduction from heteroatomic composition. Binding energy calculations indicate greater stability in the graphene-based hybrid, reflecting optimal symmetry matching at the interface. UV–Vis spectra analysis shows that graphene dominates the optical response in its hybrid system, maintaining its symmetric spectral characteristics, while CdSe QDs govern the BN hybrid’s absorption. Electrostatic potential distributions remain essentially unchanged post-hybridization, preserving the intrinsic charge symmetry of components. Two-photon absorption (TPA) characterization reveals significant nonlinear optical properties in CdSe QDs, particularly at the first excited state. This work provides the first systematic comparison of charge transfer dynamics in CdSe QDs hybridized with graphene versus BN, demonstrating how material symmetry governs optoelectronic modulation mechanisms. The findings establish symmetry–property relationships that inform the design of low-dimensional hybrid materials for photonic applications. Full article

The Co(II) complex [CoCl₂(AImd)₂] (AImd = 1-allylimidazole) was reinvestigated using a combination of experimental and theoretical methods. The previously reported crystal structure was redetermined and Hirshfeld surface analysis and enrichment ratios were added showing that intermolecular H⋯Cl and π⋯π interactions are the primary forces in the crystal structure, while H⋯H interactions dominate the surface of the molecule, making it rather hydrophobic in keeping with a low solubility in water. A Quantum Theory of Atoms in Molecules (QTAIM)/Non-Covalent Interactions (NCI)-Reduced Density Gradient (RDG) analysis on a dimeric model showed that the energies V(r) of the classical H⋯Cl hydrogen bonds range from −3.64 kcal/mol to −0.75 kcal/mol and were augmented by hydrophobic H⋯C interactions of >1 kcal/mol. T-dependent magnetization measurements reveal paramagnetic behavior with an effective magnetic moment of µ_eff = 4.66(2) µ_B. UV-vis absorption spectra in solution showed intense absorptions peaking at 240 nm, corresponding to intraligand π→π* transitions within the 1-allylimidazole moiety and a structured absorption around 600 nm, which is attributed to the spin-allowed d→d transitions of the high-spin Co(II) d⁷ ion in a distorted tetrahedral geometry. Both assignments were confirmed through TD-DFT calculations on the electronic transitions and agree with the DFT-calculated compositions of the frontier molecular orbitals. Molecular docking to hypoxia-inducible factor-1 alpha (HIF-1α) gave a docking score of −5.48 kcal/mol and showed hydrophobic⋯hydrophobic π-stacking interactions with the Ile233, Leu243, Val338, and Leu262 residues. A higher docking score of −6.11 kcal/mol and predominant hydrophobic⋯hydrophobic interactions with Trp296, His279, and Ile281 were found for HIF-1 inhibiting factor (FIH-1). Full article

The persistent contamination of aquatic environments by heavy metals, particularly Pb²⁺, Cd²⁺, and Cu^2+, poses a serious global threat due to their toxicity, persistence, and bioaccumulative behavior. In response, low-cost and eco-friendly adsorbents are being explored, among which CaCO₃-based biocomposites derived from mollusk shells have shown exceptional performance. In this study, a hybrid biocomposite composed of poly(vinyl alcohol) (PVA) and oyster shell-derived CaCO₃ was computationally investigated using Density Functional Theory (DFT) to elucidate the electronic and structural basis for its high metal-removal efficiency. Calculations were performed at the B3LYP/6-311++G(d,p), M05-2X/6-311+G(d,p), and M06-2X/6-311++G(d,p) levels using GAUSSIAN 16. Among them, B3LYP was identified as the most balanced in terms of accuracy and computational cost. The hybridization with CaCO₃ reduced the HOMO-LUMO gap by 20% and doubled the dipole moment (7.65 Debye), increasing the composite’s polarity and reactivity. Upon chelation with metal ions, the gap further dropped to as low as 0.029 eV (Cd²⁺), while the dipole moment rose to 17.06 Debye (Pb²⁺), signaling enhanced charge separation and stronger electrostatic interactions. Electrostatic potential maps revealed high nucleophilicity at carbonate oxygens and reinforced electrophilic fields around the hydrated metal centers, correlating with the affinity trend Cu²⁺ > Cd²⁺ > Pb²⁺. Fukui function analysis indicated a redistribution of reactive sites, with carbonate oxygens acting as ambiphilic centers suitable for multidentate coordination. Natural Bond Orbital (NBO) analysis confirmed the presence of highly nucleophilic lone pairs and weakened bonding orbitals, enabling flexible adsorption dynamics. Furthermore, NCI/RDG analysis highlighted attractive noncovalent interactions with Cu²⁺ and Pb²⁺, while FT-IR simulations demonstrated the formation of hydrogen bonding (O–H···O=C) and Ca²⁺···O coordination bridges between phases. Full article

Polymethyl methacrylate (PMMA) is a polymer with excellent properties for water remediation. Understanding the molecular interactions between pharmaceuticals, such as β-blockers, and PMMA is essential for optimizing purification technologies. Atomistic calculations provide a detailed understanding of the interaction between molecules without the need for expensive equipment. This study presents a computational analysis of how PMMA interacts with salbutamol and atenolol. Geometrical optimizations were performed using semiempirical and density functional theory (DFT) calculations. To identify interactions between PMMA and pharmaceuticals, we employed the reduced density gradient (RDG) approach, providing insight into intramolecular noncovalent interactions between PMMA’s atoms and pharmaceuticals. Full article

A theoretical investigation utilizing density functional theory (DFT) calculations was conducted to explore the coordination complexes formed between histidine (His) ligands and various divalent transition metal ions (Mn²⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺). Conformational exploration of the His ligand was initially performed to assess its stability upon coordination. Both 1:1 and 1:2 of metal-to-ligand complexes were scrutinized to elucidate their structural features and the relative stability of the complexes. This study examined the ability of His to act as a bidentate or tridentate coordinating ligand, along with the differences in coordination geometry when solvent effects were incorporated. The reduced density gradient (RDG) analysis and local electron attachment energy (LEAE) analysis were employed to elucidate the interaction planes and the nucleophilic and electrophilic properties. The electronic properties were analyzed through electrostatic potential (ESP) maps and natural population analysis (NPA) of atomic charge distributions. This computational study provides valuable insights into the diverse coordination modes of His and its interactions with divalent transition metal ions, contributing to a better understanding of the role of this amino acid ligand in the formation of transition metal complexes. The findings can aid in the design and construction of self-assembled structures involving His-metal coordination. Full article

Thiadiazole (THD) derivatives are famous for their exceptional chemical properties and versatile biological activities. In this work, we report computational investigations of the structure, reactivity, and binding affinity of three 1,3,4-THD derivatives (THDs) toward the SARS-CoV-2 main protease (Mpro). Hirshfeld surface (HS) analyses are carried out in conjunction with topological calculations in the context of the quantum theory of atoms in molecules (QTAIM) and reduced density gradient (RDG) to unravel the nature and magnitude of noncovalent interactions that contribute to maintaining these THDs. The three approaches consistently indicate that the titled THDs are mainly stabilized by weak intramolecular H…H, C-H…π, C-H…N, and N-H..H interactions in their monomeric forms, while their dimers also exhibit intermolecular π…π stacking and T-shaped contacts. In addition, Hirshfeld atomic charges, frontier molecular orbitals (FMOs), Fukui functions, and molecular electrostatic potential (MEP) reveal that the pyrrolic H atom (ring F) and the imidazole N atom (ring E) are the preferred binding sites for nucleophilic and electrophilic attacks, respectively. Finally, docking and molecular dynamics simulations demonstrate the remarkable binding profile of THDs toward the Mpro, which can be related to potential inhibitory activity. Full article

In our current investigation, we employed a B₁₂N₁₂ nanocage to extract paracetamol from water utilizing a DFT approach. We explored three distinct positions of paracetamol concerning its interaction with the B₁₂N₁₂ nanocage, designated as complex-1 (BNP-1), complex-2 (BNP-2), and complex-3 (BNP-3), under both aqueous and gaseous conditions. The optimized bond distances exhibited strong interactions between the nanocage and the paracetamol drug in BNP-1 and BNP-3. Notably, BNP-1 and BNP-3 displayed substantial chemisorption energies, measuring at −27.94 and −15.31 kcal/mol in the gas phase and −30.69 and −15.60 kcal/mol in the aqueous medium, respectively. In contrast, BNP-2 displayed a physiosorbed nature, indicating weaker interactions with values of −6.97 kcal/mol in the gas phase and −4.98 kcal/mol in the aqueous medium. Our analysis of charge transfer revealed significant charge transfer between the B₁₂N₁₂ nanocage and paracetamol. Additionally, a Quantum Theory of Atoms in Molecules (QTAIM) analysis confirmed that the O─B bond within BNP-1 and BNP-3 exhibited a strong covalent and partial bond, encompassing both covalent and electrostatic interactions. In contrast, the H─N bond within BNP-2 displayed a weaker hydrogen bond. Further investigation through Noncovalent Interaction (NCI) and Reduced Density Gradient (RDG) analyses reinforced the presence of strong interactions in BNP-1 and BNP-3, while indicating weaker interactions in BNP-2. The decrease in the electronic band gap (E_g) demonstrated the potential of B₁₂N₁₂ as a promising adsorbent for paracetamol. Examining thermodynamics, the negative values of ∆H (enthalpy change) and ∆G (Gibbs free energy change) pointed out the exothermic and spontaneous nature of the adsorption process. Overall, our study underscores the potential of B₁₂N₁₂ as an effective adsorbent for eliminating paracetamol from wastewater. Full article

Essential oils are volatile oil-like liquids with a characteristic strong smell and taste. They are formed in plants and are then extracted. Essential oils have extremely strong physiological and pharmacological properties, which are used in the medicine, cosmetics, and food industries. In this study, the molecules caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene, which are the molecules with the highest contents in the essential oil of the plant mentioned in the title, were selected and theoretical calculations describing their interactions with water were performed. Because oil–water mixtures are very important in biology and industry and are ubiquitous in nature, quantum chemical calculations for binary mixtures of water with caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene were performed using the density functional theory (DFT)/B3LYP method with a basis of 6–31 G (d, p). Molecular structures, HOMO–LUMO energies, electronic properties, reactivity (ELF, LOL, and Fukui), and NCI-RDG and molecular electrostatic potential (MEP) on surfaces of the main components of Phlomis bruguieri Desf. essential oil were calculated and described. Full article

In this paper, both methods (DFT and HF) were used in a theoretical investigation of 3-bromo-2-Hydroxypyridine (3-Br-2HyP) molecules where the molecular structures of the title compound have been optimized. Molecular electrostatic potential (MEP) was computed using the B3LYP/6-311++G(d,p) level of theory. The time-dependent density functional theory (TD-DFT) approach was used to simulate the HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) on the one hand to achieve the frontier orbital gap and on the other hand to calculate the UV–visible spectrum of the compound in gas phase and for different solvents. In addition, electronic localization function and Fukui functions were carried out. Intermolecular interactions were discussed by the topological AIM (atoms in molecules) approach. The thermodynamic functions have been reported with the help of spectroscopic data using statistical methods revealing the correlations between these functions and temperature. To describe the non-covalent interactions, the reduced density gradient (RDG) analysis is performed. To study the biological activity of the compound of the molecule, molecular docking studies were executed on the active sites of BRD2 inhibitors and to explore the hydrogen bond interaction, minimum binding energies with targeted receptors such as PDB ID: 5IBN, 3U5K, 6CD5 were calculated. Full article

The physicochemical properties of binary systems are of great importance for the application of the latter. We report on the investigation of an ammonium sulfamate–urea binary system with different component ratios using a combination of experimental (FTIR, XRD, TGA/DSC, and melting point) and theoretical (DFT, QTAIM, ELF, RDG, ADMP, etc.) techniques. It is shown that, at a temperature of 100 °C, the system under study remains thermally and chemically stable for up to 30 min. It was established using X-ray diffraction analysis that the heating time barely affects the X-ray characteristics of the system. Data on the aggregate states in specified temperature ranges were obtained with thermal analysis and determination of the melting point. The structures of the ammonium sulfamate–urea system with different component ratios were optimized within the density functional theory. The atom-centered density matrix propagation calculation of the ammonium sulfamate–urea system with different component ratios was performed at temperatures of 100, 300, and 500 K. Regardless of the component ratio, a regular increase in the potential energy variation (curve amplitude) with an increase in temperature from 100 to 500 K was found. Full article

The title compound triphenyl tetrazolium (TPT) of phenobarbital, 5-Ethyl-5-phenylbarbituric acid triphenyl tetrazolium salt (4) was prepared by the reaction of 5-Ethyl-5-phenyl-2,4,6(1H, 3H, 5H)-pyrimidinetrione, monosodium salt (1) with triphenyl tetrazolium chloride (3) in deionized water at an ambient temperature through a cation exchange reaction. Colorless crystals of compound four suitable for an X-ray structural analysis were obtained by slow evaporation from acetonitrile. Compound four had crystallized in the monoclinic space group, P_21/c, with a = 15.3678 (9) Å, b = 12.2710 (7) Å, c = 21.8514 (13) Å, β = 109.867 (2)°, V = 3875.5 (4) ų, and Z = 4. A Through density functional theory (DFT) calculations, the probable molecular association structure in the phenobarbitone -triphenyl tetrazolium solution was studied. With the 6-311G-(d,p) basis set, the gas phase features of the phenobarbital-triphenyl tetrazolium clusters with a phenobarbitone dimer and water molecules, including an optimum structure and intermolecular hydrogen bonding, were investigated in detail. In addition, the positions and strengths of the intermolecular hydrogen bond interactions between the phenobarbitone and triphenyl tetrazolium molecules were analyzed using atoms in molecule (AIM) analysis, reduced density gradient (RDG) methods, the XRD method, and the non-covalent interaction (NCI) index method. In addition, the molecular electrostatic potential (MEP) surfaces were analyzed to determine the electrophilic and nucleophilic centers. Full article

Imidazole derivatives have found wide application in organic and medicinal chemistry. In particular, benzimidazoles have proven biological activity as antiviral, antimicrobial, and antitumor agents. In this work, we experimentally and theoretically investigated N-Butyl-1H-benzimidazole. It has been shown that the presence of a butyl substituent in the N position does not significantly affect the conjugation and structural organization of benzimidazole. The optimized molecular parameters were performed by the DFT/B3LYP method with 6-311++G(d,p) basis set. This level of theory shows excellent concurrence with the experimental data. The non-covalent interactions that existed within our compound N-Butyl-1H-benzimidazole were also analyzed by the AIM, RDG, ELF, and LOL topological methods. The color shades of the ELF and LOL maps confirm the presence of bonding and non-bonding electrons in N-Butyl-1H-benzimidazole. From DFT calculations, various methods such as molecular electrostatic potential (MEP), Fukui functions, Mulliken atomic charges, and frontier molecular orbital (HOMO-LUMO) were characterized. Furthermore, UV-Vis absorption and natural bond orbital (NBO) analysis were calculated. It is shown that the experimental and theoretical spectra of N-Butyl-1H-benzimidazole have a peak at 248 nm; in addition, the experimental spectrum has a peak near 295 nm. The NBO method shows that the delocalization of the aσ-electron from σ (C1–C2) is distributed into antibonding σ* (C1–C6), σ* (C1–N26), and σ* (C6–H11), which leads to stabilization energies of 4.63, 0.86, and 2.42 KJ/mol, respectively. Spectroscopic investigations of N-Butyl-1H-benzimidazole were carried out experimentally and theoretically to find FTIR vibrational spectra. Full article