Search Results (253)

The crystal structures of the 2-amino-5-halogenopyridines (halogen = Cl (1), Br (2)) and 2,3-diamino-5-halogenopyridines (halogen = Cl (3), Br (4)) were compared with respect to their intermolecular interactions. An ab-initio-based method for evaluating the interaction energies between molecules was employed to estimate the driving forces of crystal formation. As a result, regularities in crystal structure organization were identified. For compounds 1 and 2, a dimeric building unit is formed by two N–H…N_pyr hydrogen bonds. These dimers are further connected to neighboring units by C–H…π, C–H…N, N…X (X = Cl, Br), and non-specific interactions. The aforementioned intermolecular interactions give rise to layered structures that are similar but not isotypical. No significant contributions from π–π or N–H…N(H₂) interactions are observed in 1 and 2. The structures of 3 and 4 are isotypical and crystallize in the non-centrosymmetric space group P2₁2₁2₁. The most important intermolecular interactions are N–H…N_pyr, N–H…N(H₂), and stacking interactions. These interactions lead to identical columnar-layered structures in both 3 and 4. No significant contributions from halogen bonds of the type N…X (X = Cl, Br) are found in 3 and 4. Full article

A series of water-soluble molecules based on 8-isopropyl-2-methyl-5-nitroquinoline and 1,10-phenanthroline core were designed by introducing a π-conjugated bridge, vinyl unit –CH=CH–. We present the selective conversion of methyl groups located on the C2 and C9 positions in the constitution of selected quinoline or 1,10-phenanthroline derivatives, respectively, into vinyl (or styryl) products by applying Perkin condensation. The two groups of ligands differ in the presence of one or two arms. The structure of the molecule ((1E,1′E)-(1,10-phenanthroline-2,9-diyl)bis(ethene-2,1-diyl))bis(benzene-4,1,3-triyl) tetraacetate was determined by single-crystal X-ray diffraction measurements. The X-ray, NMR, and DFT computational studies indicate the influence of rotation (rotamers) on the physical properties of studied styryl molecules. The results show that the styryl molecules with the vinyl unit –CH=CH– exhibit significant static and dynamic hyperpolarizabilities. Quantum chemical calculations using density functional theory and B3LYP/6-311++G(d,p) with Grimme’s dispersion correction approach predict the existence and relative stability of different spatial cis(Z)- and trans(E)-conformers of styryl derivatives of quinoline and 1,10-phenanthroline, which exhibit different electronic distribution and conjugation within the molecular skeleton, dipole moments, and steric interactions, leading to variations in their photophysical behavior and various applications. Our studies indicate that the rotation and isomerization of aryl groups can significantly influence the electronic and optical properties of π-conjugated systems, such as vinyl units (–CH=CH–). The rotation of aryl groups around the single bond that connects them to the vinyl unit can lead to changes in the effective π-conjugation between the aryl group and the rest of the π-conjugated system. The rotation and isomerization of aryl groups in π-conjugated systems significantly impact their electronic and optical properties. These changes can modify the efficiency of π-conjugation, affecting charge transfer processes, absorption properties, light emission, and electrical conductivity. In designing optoelectronic materials, such as organic dyes, organic semiconductors, or electrochromic materials, controlling the rotation and isomerization of aryl groups can be crucial for optimizing their functionality. Full article

Developing organic luminescent materials with the advantages of low cost, high thermal stability, and strong emission performance is incredibly desirable. In this work, we synthesized a new neutral heteroleptic Cu(I) complex characterized by single-crystal X-ray diffraction, FT-IR, NMR, and MALDI-TOF-MS. The neutral heteroleptic Cu(I) complex has a typical distorted tetrahedral configuration, and the complex molecules are connected into 1D chains via C-H···π interactions in crystal. Full article

The SARS-CoV-2 main protease (Mpro), essential for viral replication, remains a prime target for antiviral drug design against COVID-19 and related coronaviruses. In this study, we present a systematic investigation into the molecular determinants of Mpro inhibition using an integrated approach combining large-scale data mining, cheminformatics, and quantum chemical calculations. A curated dataset comprising 963 high-resolution structures of Mpro–ligand complexes—348 covalent and 615 non-covalent inhibitors—was mined from the Protein Data Bank. Cheminformatics analysis revealed distinct physicochemical profiles for each inhibitor class: covalent inhibitors tend to exhibit higher hydrogen bonding capacity and sp³ character, while non-covalent inhibitors are enriched in aromatic rings and exhibit greater aromaticity and lipophilicity. A novel descriptor, Weighted Hydrogen Bond Count (WHBC), normalized for molecular size, revealed a notable inverse correlation with aromatic ring count, suggesting a compensatory relationship between hydrogen bonding and π-mediated interactions. To elucidate the energetic underpinnings of molecular recognition, 40 representative inhibitors (20 covalent, 20 non-covalent) were selected based on principal component analysis and aromatic ring content. Quantum mechanical calculations at the double-hybrid B2PLYP/def2-QZVP level quantified non-bonded interaction energies, revealing that covalent inhibitors derive binding strength primarily through hydrogen bonding (~63.8%), whereas non-covalent inhibitors depend predominantly on π–π stacking and CH–π interactions (~62.8%). Representative binding pocket analyses further substantiate these findings: the covalent inhibitor F2F-2020198-00X exhibited strong hydrogen bonds with residues such as Glu166 and His163, while the non-covalent inhibitor EDG-MED-10fcb19e-1 engaged in extensive π-mediated interactions with residues like His41, Met49, and Met165. The distinct interaction patterns led to the establishment of pharmacophore models, highlighting key recognition motifs for both covalent and non-covalent inhibitors. Our findings underscore the critical role of aromaticity and non-bonded π interactions in driving binding affinity, complementing or, in some cases, substituting for hydrogen bonding, and offer a robust framework for the rational design of next-generation Mpro inhibitors with improved selectivity and resistance profiles. Full article

The crystal structures of naphthalene dicarboxamides, namely 1,4-naphthalene dicarboxamide (1,4-NDA), 2,6-naphthalene dicarboxamide (2,6-NDA), and 2,7-naphthalene dicarboxamide (2,7-NDA), are presented for the first time, along with an analysis of their supramolecular organization. The compounds, obtained in single-crystalline form via solvothermal crystallization from methanol, are stable in air to near 350 °C and have melting points above 300 °C. In their densely packed structures (ρ = 1.43–1.47 cm³g⁻¹) the combination of ${\mathrm{C}}_1^1$ (4) chains and ${\mathrm{R}}_2^2$(8) rings generates one-dimensional hydrogen-bonded ladders, with an additional ${\mathrm{R}}_4^2$(8) pattern. The amide groups and the naphthalene rings form dihedral angles between 22° and 40°. Neighboring H-bond ladders run parallel in 1,4-NDA and 2,6-NDA and are connected by means of the naphthalenedyil cores so that two-dimensional (2D) H-bonded sheets are obtained. Except for a weak intra-sheet π–π stacking in 1,4-NDA, there are no π–π stacking and C–H⋯π interactions. The ${\mathrm{R}}_2^2$(8) rings act as four-connected nodes, leading to the formation of two-dimensional H-bonded planar sheets with sql topology for the nearly linear dicarboxamides 1,4-NDA and 2,6-NDA and cds topology for the angular 2,7-NDA. Hirshfeld surface analysis and NCI plots provide additional insight into the H-bonding interactions. Full article

Industrial hemp (Cannabis sativa L.) was investigated as a sustainable biosorbent for removing Congo Red (CR) and Remazol Brilliant Blue R (RBBR) from wastewater. The unmodified hemp biosorbent exhibited moderate but practically relevant sorption capacities (4.47 mg/g for CR; 2.44 mg/g for RBBR), outperforming several agricultural waste materials. Kinetic studies revealed rapid uptake, with CR following pseudo-first-order kinetics (t₁/₂ < 15 min) and RBBR fitting the Elovich model, indicating heterogeneous surface interactions. Equilibrium data showed CR adsorption was best described by the Temkin isotherm (R² = 0.983), while RBBR followed the Langmuir model (R² = 0.998), reflecting their distinct binding mechanisms. Thermodynamic analysis confirmed spontaneous (ΔG° < 0), exothermic (ΔH° ≈ −2 kJ/mol), and entropy-driven processes for both dyes. Molecular docking elucidated the structural basis for performance differences: CR’s stronger binding (−7.5 kcal/mol) involved weak noncovalent interaction arising from partial overlap between the π-electron cloud of an aromatic ring and σ-bonds C-C or C-H (π-σ stacking) and hydrogen bonds with cellulose, whereas RBBR’s weaker affinity (−5.4 kcal/mol) relied on weak intermolecular interaction between a hydrogen atom (from a C-H bond) and the π-electron system of an aromatic ring (C-H∙∙∙π interactions). This work establishes industrial hemp as an eco-friendly alternative for dye removal, combining renewable sourcing with multi-mechanism adsorption capabilities suitable for small-scale water treatment applications. Full article

A new complex, tetrakis(1,10-phenanthroline)-bis(succinate)-(µ₂-oxo)-bis(iron(III)) nonahydrate, [Fe₂(Phen)₄(Succinate)₂(μ-O)](H₂O)₉, was synthesized using the slow evaporation method. This study provides a comprehensive characterization of this coordination compound, focusing on its structural, spectroscopic, and thermal properties, which are relevant for applications in catalysis, material science, and chemical engineering processes. Single-crystal X-ray diffraction (XRD), Raman spectroscopy, Fourier-transform infrared (FT-IR), ultraviolet-visible (UV-Vis) spectroscopy, and thermoanalytical analyses were employed to investigate the material properties. Intermolecular interactions were further explored through Hirshfeld surface analysis. XRD results revealed a monoclinic crystal system with the C2/c space group, lattice parameters: a = 12.7772(10) Å, b = 23.0786(15) Å, c = 18.9982(13) Å, β = 93.047(2)°, V = 5594.27(7) ų, and four formulas per unit cell (Z = 4). The crystal packing is stabilized by C–H⋯O, C–O⋯H, C–H⋯π, and π⋯π intermolecular interactions, as confirmed by vibrational spectroscopy. The heteroleptic coordination environment, combining weak- and strong-field ligands, results in a low-spin state with an estimated crystal field stabilization energy of −4.73 eV. Electronic properties indicate direct allowed transitions (γ = 2) with a maximum optical band gap of 2.66 eV, suggesting potential applications in optoelectronics and photochemical processes. Thermal analysis demonstrated good stability within the 25–136 °C range, with three main stages of thermal decomposition, highlighting its potential for use in high-temperature processes. These findings contribute to the understanding of Fe(III)-based complexes and their prospects in advanced material design, catalytic systems, and process optimization. Full article

A series of three 1,3-phenylene bis-oxamides 3a–c, structurally related to the GPR35 receptor-agonist drug lodoxamide, has been synthesized by reacting the 1,3-phenylene bis-oxalamates 2a and 2b with amines. The obtained compounds were characterized by ¹H and ¹³C NMR, and IR spectroscopy, they showed characteristic signals for the aromatic, N―H, and C=O groups. Molecular structure was determined using single-crystal X-ray diffraction. The supramolecular architecture is driven by N―H···O=C, N―H···N, C—H···π, and O=C···O=C interactions depicting a supramolecular helix (3a) and tapes (3b–c). Intermolecular interactions were studied using Hirshfeld surface analysis, where N―H∙∙∙X (X = N, O) hydrogen bonding represents 30.2% to the surface of 3a and 17.8–18.8% to the surface of 3b–c. The most energetic interactions involve the amide N—H∙∙∙O hydrogen bonding, contributing in the −113.9 to −97.0 kJ mol⁻¹ range to the crystal energy, being more dispersive than electrostatic in nature. The molecular docking study was performed to evaluate the binding ability of 3a–c compounds to the GPR35 receptor, showing a favorable binding in a similar way to lodoxamide. Full article

The crystal structures, interactions, and contacts analyses of four N-(ferrocenylalkyl)benzene-carboxamide derivatives are described as the N-(ferrocenylmethyl)benzenecarboxamide 4a, N-(ferrocenylmethyl)-2,6-difluorobenzenecarboxamide 4e, N-(ferrocenylmethyl)pentafluorobenzenecarboxamide 4f and N-(ferrocenylethyl)-4-fluorobenzenecarboxamide 5. Intermolecular amide⋯amide hydrogen-bonding interactions as 1D intermolecular chains are present in all four crystal structures, with N⋯O distances ranging from 2.819 (2) to 2.924 (3) Å. Three of the crystal structures have one molecule per asymmetric unit, except the phenyl 4a, which has Z’=2. In the structure of 4a, Fc(C-H)⋯(phenyl) and _phenylC-H⋯π(C₅H₄) ring interactions dominate the interaction landscape, together with (1:1) face-to-face (phenyl)⋯(phenyl) and (C₅H₅)⋯(C₅H₅) ring stacked pairs (Fc = ferrocenyl moiety). In 4e, interlocking ferrocenyls, short C-H⋯(C-F) and C-H⋯O hydrogen bonds are the only additional notable intermolecular interactions. In the pentafluorophenyl derivative 4f, a remarkable selection of interactions is present with interwoven 1D ferrocenyl⋯(C₆F₅) stacking and C-H⋯F interactions; molecules aggregate forming impressive 1D columns comprising intertwined (Fc⋯C₆F₅⋯)_n ring stacking. In the ethyl bridged system 5, C-H⋯F and C-H⋯π (arene) contacts with (4-fluorobenzene) ring⋯ring pairs combine and stack about inversion centres. The reported para-F substituted structure REYWOU (4d) is used for comparisons with the 4a, 4e, 4f, and 5 crystal structures. In view of the rich interaction chemistry, contacts enrichment analyses of the Hirshfeld surface highlights several interesting features in all five ferrocenylalkylcarboxamide structures. Full article

The injection of CO₂ into coal reservoirs occurs in its supercritical state (ScCO₂), which significantly alters the pore structure and chemical composition of coal, thereby influencing the adsorption and diffusion behavior of methane (CH₄). Understanding these changes is crucial for optimizing CH₄ extraction and improving CO₂ sequestration efficiency. This study aims to investigate the effects of ScCO₂ on the pore structure, chemical bonds, and CH₄ diffusion mechanisms in bituminous coal to provide insights into coal reservoir stimulation and CO₂ storage. By utilizing high-pressure CO₂ injection adsorption, low-pressure CO₂ gas adsorption (LP-CO₂-GA), Fourier-transform infrared spectroscopy (FTIR), and reactive force field molecular dynamics (ReaxFF-MD) simulations, this study examines the multi-scale changes in coal at the nano- and molecular levels. The following results were found: Pore Structure Evolution: After ScCO₂ treatment, micropore volume increased by 19.1%, and specific surface area increased by 11.2%, while mesopore volume and specific surface area increased by 14.4% and 5.7%, respectively. Chemical Composition Changes: The content of aromatic structures, oxygen-containing functional groups, and hydroxyl groups decreased, while aliphatic structures increased. Specific molecular changes included an increase in (CH₂)_n, 2H, 1H, and secondary alcohol (-C-OH) and phenol (-C-O) groups, while Car-Car and Car-H bonds decreased. Mechanisms of Pore Volume Changes: The pore structure evolves through three distinct phases: Swelling Phase: Breakage of low-energy bonds generates new micropores. Aromatic structure expansion reduces intramolecular spacing but increases intermolecular spacing, causing a decrease in micropore volume and an increase in mesopore volume. Early Dissolution Phase: Continued bond breakage increases micropore volume, while released aliphatic and aromatic structures partially occupy these pores, converting some mesopores into micropores. Later Dissolution Phase: Minimal chemical bond alterations occur, but weakened π-π interactions and van der Waals forces between aromatic layers result in further mesopore volume expansion. Impact on CH₄ Diffusion: Changes in pore volume directly affect CH₄ migration. In the early stages of ScCO₂ interaction, pore shrinkage reduces the mean square displacement (MSD) and self-diffusion coefficient of CH₄. However, as the reaction progresses, pore expansion enhances CH₄ diffusion, ultimately improving gas extraction efficiency. This study provides a fundamental understanding of how ScCO₂ modifies coal structure and CH₄ transport properties, offering theoretical guidance for enhanced CH₄ recovery and CO₂ sequestration strategies. Full article

Diaryl ureas (DU) are a cornerstone scaffold in organic and medicinal chemistry, celebrated for their unique structural attributes and broad range of biomedical applications. Their therapeutic reach has broadened beyond kinase inhibition in cancer therapy to encompass diverse mechanisms, including modulation of chromatin remodeling complexes, interference with developmental signaling pathways, and inhibition of stress-activated protein kinases in inflammatory disorders. A critical element in the rational design and optimization of DU-based therapeutics is a detailed understanding of their molecular recognition by target proteins. In this study, we employed a multi-tiered computational approach to investigate the molecular determinants of DU–protein interactions. A large-scale data mining of the Protein Data Bank resulted in an in-house dataset of 158 non-redundant, high-resolution crystal structures of DU–protein complexes. This dataset serves as the basis for a systematic analysis of nonbonded interactions, including hydrogen bonding, salt bridges, π–π stacking, CH-π, cation–π, and XH-π interactions (X = OH, NH, SH). Advanced electronic structure calculations at the B2PLYP/def2-QZVP level are applied to quantify the energetic contributions of these interactions and their roles in molecular recognition of diaryl ureas in their target proteins. The study led to the following findings: central to the molecular recognition of diaryl ureas in proteins are nonbonded π interactions—predominantly CH-π and π–π stacking—that synergize with hydrogen bonding to achieve high binding affinity and specificity. Aromatic R groups in diaryl ureas play a pivotal role by broadening the interaction footprint within hydrophobic protein pockets, enabling energetically favorable and diverse binding modes. Comparative analyses highlight that diaryl ureas with aromatic R groups possess a more extensive and robust interaction profile than those with non-aromatic counterparts, emphasizing the critical importance of nonbonded π interactions in molecular recognition. These findings enhance our understanding of molecular recognition of diaryl ureas in proteins and provide valuable insights for the rational design of diaryl ureas as potent and selective inhibitors of protein kinases and other therapeutically significant proteins. Full article

Two new Co(II) coordination compounds viz. [Co(H₂O)(bz)₂(μ-3-Ampy)₂]_n (1) and [Co(4-Mebz)₂(2-Ampy)₂] (2) (wherebz = benzoate, 4-Mebz = 4-Methylbenzoate and Ampy = Aminopyridine) were synthesized and characterized via elemental (CHN), electronic spectroscopy, FT-IR spectroscopy, and thermogravimetric analysis (TGA). The molecular structures were determined by single-crystal X-ray diffraction analysis, inferring that compound 1 crystallizes as a 3-Ampy bridged Co(II) coordination polymer, whereas compound 2 crystallizes as a mononuclear Co(II) compound. Compound 1 unfolds the presence of N–H⋯O, C–H⋯O, O–H⋯O, C–H⋯N and aromatic π⋯π interactions, while for compound 2, N–H⋯O, C–H⋯O, C–H⋯C and C–H⋯π interactions are observed. Both the compounds showcase scarcely reported chelate ring interactions involving the benzoate moiety (chelate ring⋯π in 1 and N–H⋯chelate ring in 2). We also conducted theoretical evaluations comprising of combined QTAIM/NCI plot analysis, DFT energy calculation and MEP surface analysis to analyze the supramolecular interactions present in the crystal structures. As per QTAIM parameters, the predominance of π-stacking interactions over hydrogen bonds in stabilizing the assembly in compound 1 is affirmed. Likewise, in compound 2, both hydrogen bonding (HBs) and C–H⋯π interactions are deemed pivotal in stabilizing the dimeric assemblies. The in vitro antiproliferative activities of compounds 1 and 2 were performed against Dalton’s lymphoma (DL) cancer cell lines through cytotoxicity and apoptosis assays, showcasing higher cytotoxicity of compound 1 (IC₅₀ = 28 μM) over compound 2 (IC₅₀ = 34 μM). Additionally, a molecular docking study investigated the structure–activity relationship of these compounds and allowed an understanding of the molecular behaviour after treatment. Full article

Arsenic (As), a highly toxic and carcinogenic heavy metal, poses significant risks to soil and water quality, while oxytetracycline (OTC), a widely used antibiotic, contributes to environmental pollution due to excessive human usage. Addressing the coexistence of multiple pollutants in the environment, this study investigates the simultaneous adsorption of As(III) and OTC using a novel bimetallic zinc-iron-modified biochar (1Zn-1Fe-1SBC). The developed adsorbent demonstrates enhanced recovery, improved adsorption efficiency, and cost-effective operation. Characterization results revealed a high carbon-to-hydrogen ratio (C/H) and a specific surface area of 1137 m² g⁻¹ for 1Zn-1Fe-1SBC. Isotherm modeling indicated maximum adsorption capacities of 34.7 mg g⁻¹ for As(III) and 172.4 mg g⁻¹ for OTC. Thermodynamic analysis confirmed that the adsorption processes for both pollutants were spontaneous (ΔG < 0), endothermic (ΔH > 0), and driven by chemical adsorption (ΔH > 80 kJ mol⁻¹), with increased system disorder (ΔS > 0). The adsorption mechanisms involved multiple interactions, including pore filling, hydrogen bonding, electrostatic attraction, complexation, and π-π interactions. These findings underscore the potential of 1Zn-1Fe-1SBC as a promising adsorbent for the remediation of wastewater containing coexisting pollutants. Full article

The direct discharge of cationic surfactants into environmental matrices has exponentially increased due to their wide application in many products. These compounds and their degraded products disrupt microbial dynamics, hinder plant survival, and affect human health. Therefore, there is an urgent need to develop electroanalytical assessment techniques for their identification, determination, and monitoring. In our study, ZnO-PANI nanocomposites were electrodeposited on a glassy carbon electrode (GCE), followed by the immobilization of laccase enzymes and the electrodeposition of polypyrrole (PPy), to form a biosensor that was used for the detection of CTAB. A UV-Vis analysis showed bands corresponding to the π-π* transition of benzenoid and quinoid rings, π-polaron band transition and n-π*polaronic transitions associated with the extended coil chain conformation of PANI, and the presence and interaction of ZnO with PANI and type 3 copper in the laccase enzymes. The FTIR analysis exhibited peaks corresponding to N-H and C-N stretches and bends for amine, C=C stretches for conjugated alkenes, and a C-H bend for aromatic compounds. A high-resolution scanning electron microscopy (HRSEM) analysis proved that PANI and ZnO-PANI were deposited as fibres with hairy topography resulting from covalent bonding with the laccase enzymes. The modified electrode (PPy-6/GCE) was used as a platform for the detection of CTAB with three linear ranges of 0.5–100 µM, 200–500 µM, and 700–1900 µM. The sensor displayed a high sensitivity of 0.935 μA μM⁻¹ cm⁻², a detection limit of 0.0116 µM, and acceptable recoveries of 95.02% and 87.84% for tap water and wastewater, respectively. Full article

Chalcogen bonds (ChBs) involving selenium have attracted substantial scholarly interest in past years owing to their fundamental roles in various chemical and biological fields. However, the effect of the valency state of the electron-deficient selenium atom on the characteristics of such ChBs remains unexplored. Herein, we comparatively studied the σ-hole-type Se∙∙∙O ChBs between SeF₂/SeF₄ and a series of oxygen-bearing Lewis bases, including water, methanol, dimethyl ether, ethylene oxide, formaldehyde, acetaldehyde, acetone, and formic acid, using ab initio computations. The interaction energies of these chalcogen-bonded heterodimers vary from −5.25 to −11.16 kcal/mol. SeF₂ participates in a shorter and stronger ChB than SeF₄ for all the examined heterodimers. Such Se∙∙∙O ChBs are closed-shell interactions, exhibiting some covalent character for all the examined heterodimers, except for SeF₄∙∙∙water. Most of these chalcogen-bonded heterodimers are predominantly stabilized through orbital interactions between the lone pair of the O atom in Lewis bases and the σ*(Se–F) antibonding orbitals of Lewis acids. The back-transfer of charge from the lone pair of selenium into the σ* or π* antibonding orbitals of Lewis bases is also observed for all systems. Energy decomposition analysis reveals that the electrostatic component significantly stabilizes the targeted heterodimers, while the induction and dispersion contributions cannot be ignored. Full article