Search Results (194)

Using density functional theory (M06-2X-D3/def2-TZVP), we investigated the 1,2-addition reactions of NH₃ with a series of heavy imine analogues, G13=P-Rea (where G13 denotes a Group 13 element; Rea = reactant), featuring a mixed G13–P–Ga backbone. Theoretical analyses revealed that the bonding nature of the G13=P moiety in G13=P-Rea molecules varies with the identity of the Group 13 center. For G13=B, Al, Ga, and In, the bonding is best described as a donor–acceptor (singlet–singlet) interaction, whereas for G13 = Tl, it is characterized by an electron-sharing (triplet–triplet) interaction. According to our theoretical studies, all G13=P-Rea species—except the Tl=P analogue—undergo 1,2-addition with NH₃ under favorable energetic conditions. Energy decomposition analysis combined with natural orbitals for chemical valence (EDA–NOCV), along with frontier molecular orbital (FMO) theory, reveals that the primary bonding interaction in these reactions originates from electron donation by the lone pair on the nitrogen atom of NH₃ into the vacant p-π* orbital on the G13 center. In contrast, a secondary, weaker interaction involves electron donation from the phosphorus lone pair of the G13=P-Rea species into the empty σ* orbital of the N–H bond in NH₃. The calculated activation barriers are primarily governed by the deformation energy of ammonia. Specifically, as the atomic weight of the G13 element increases, the atomic radius and G13–P bond length also increase, requiring a greater distortion of the H₂N–H bond to reach the transition state. This leads to a higher geometrical deformation energy of NH₃, thereby increasing the activation barrier for the 1,2-addition reaction involving these Lewis base-stabilized, heavy imine-like G13=P-Rea molecules and ammonia. Full article

The one-dimensional (1D) Sb(III)-based organic–inorganic hybrid perovskite (AImd)₂¹_∞[SbI₅] (AImd = 1-allylimidazolium) crystallizes in the orthorhombic, centrosymmetric space group Pnma. The structure consists of corner-sharing [SbI₆] octahedra forming 1D chains separated by allylimidazolium cations. Void analysis through Mercury CSD software confirmed a densely packed lattice with a calculated void volume of 1.1%. Integrated quantum theory of atoms in molecules (QTAIM) and non-covalent interactions index (NCI) analyses showed that C–H···I interactions between the cations and the ¹_∞[SbI₅]²⁻ network predominantly stabilize the supramolecular assembly followed by N–H···I hydrogen bonds. The calculated growth morphology (GM) model fits very well to the experimental morphology. UV–Vis diffuse reflectance spectroscopy allowed us to determine the optical band gap to 3.15 eV. Density functional theory (DFT) calculations employing the B3LYP, CAM-B3LYP, and PBE0 functionals were benchmarked against experimental data. CAM-B3LYP best reproduced Sb–I bond lengths, while PBE0 more accurately captured the HOMO–LUMO gap and the associated electronic descriptors. These results support the assignment of an inorganic-to-organic [Sb–I] → π* charge-transfer excitation, and clarify how structural dimensionality and cation identity shape the material’s optoelectronic properties. Full article

Molybdenum lithium compounds and materials are being researched and applied in cutting-edge industries; however, their bonding has not been explored in a systematic way. The present study investigates the MoLi molecule, to shed light on its bonding. Specifically, the electronic structure and bonding of the ground and 40 low-lying states of the MoLi molecule are explored, employing multireference methodologies, i.e., CASSCF and MRCISD(+Q) in conjunction with the aug-cc-pV5z(-PP) basis set. Bond distances, dissociation energies, dipole moments as well as common spectroscopic constants are given, while the potential energy curves are plotted. For the ground state, X${}^6\Sigma _{+}$, it is found that $R_{\mathrm{e}}$ = 2.708 Å, $D_{\mathrm{e}}$ = 24.1 kcal/mol, ${\omega }_{\mathrm{e}}$ = 316.8 ${\mathrm{cm}}^{-1}$, ${\omega }_{\mathrm{e}}{x}_{\mathrm{e}}$ = 2.11 ${\mathrm{cm}}^{-1}$, and μ = 3.63 D. Overall, the calculated states present a variety of bonds, from weak van der Waals up to the formation of 2.5 bonds. The dissociation energies of the calculated states range from 2.3 kcal/mol ($\mathrm{a}{}^8{\Sigma }^{+}$) to 34.7 ($\mathrm{c}{}^4\Pi$), while the bond distances range from 2.513 Å to 3.354 Å. Finally, dipole moment values up to 3.72 D are calculated. In most states, a 2s${2\mathrm{p}}_{\mathrm{z}}$ hybridization on Li and a ${4\mathrm{d}}_{{\mathrm{z}}^2}$5s${5\mathrm{p}}_{\mathrm{z}}$ or 5s${5\mathrm{p}}_{\mathrm{z}}$ hybridization on Mo are found. Moreover, it is observed that the excited Li(${}^2\mathrm{P}$) atom forms the shortest bonds because its empty ${2\mathrm{s}}^0$ orbital can easily accept electrons, resulting in a strong σ dative bond. Finally, the present work highlights the exceptional ability of lithium atoms to participate in a variety of bonding schemes, and it could provide the opening gate for further investigation of this species or associated material and complexes. Full article

G-protein-coupled receptors (GPCRs) are a group of various membrane proteins that mediate essential physiological processes by translating extracellular signals into intracellular responses. The β2-Adrenergic Receptor (β2-AR), a key GPCR, plays a critical role in smooth muscle relaxation, bronchodilation, and cardiovascular function, making it an important therapeutic target for diseases such as asthma and hypertension. Diketopiperazines (DPKs), as cyclic peptides, have shown promise as scaffolds for inhibiting protein interactions and modulating receptor activity, offering a potential alternative to traditional small-molecule inhibitors with reduced side effects. In this study, five DPK derivatives were selected from the PubChem database and evaluated for their binding affinity to the 3D structure of β2-AR (PDB ID = 2RH1) through molecular docking studies using AutoDock 4.6 and MGLTools. The binding energy and hydrogen bond formation of each compound were evaluated to determine their interaction efficiency. Among the compounds, tryptophan-proline diketopiperazine (compound 3) exhibited the highest binding affinity with a binding energy of −5.89 kcal/mol. This enhanced interaction is attributed to the aromatic nature of tryptophan, which promotes strong π-π stacking interactions, and the rigidity of proline, which optimally fits within the receptor’s binding pocket. Hydrophobic interactions further stabilized the complex. These findings highlight compound 3 as a promising β2-AR modulator, providing valuable insights for the design of peptide-based inhibitors targeting β2-AR-related pathologies. 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

Micron-sized, ultrathin metal–organic framework (MOF) sheet is a two-dimensional (2D) hybrid material with a large specific surface area, which can be used not only in the fields of energy and biomedicine, but also in electrode modification to improve the electrochemical detection effect. In this work, the 2D-structured Co-TCPP(Fe) MOF sheets were synthesized from porphyrin molecules and cobalt ions and then combined with reduced graphene oxide (rGO) and perfluorosulfonic acid polymer (Nafion) solution to construct Co-TCPP(Fe)/rGO/Nafion-modified electrodes capable of sensitively capturing dopamine (DA). The 2D ultrathin lamellar structure of this electrode-modified material is beneficial to the formation of π-π stacking effect with DA molecules, and the oxygen-containing groups carried on its surface can also form electrostatic attraction with the amino groups of DA molecules. Therefore, the Co-TCPP(Fe)/rGO/Nafion-modified electrode under the synergistic effect shows a specific adsorption effect on DA molecules, resulting in high anti-interference ability and a low detection limit of 0.014 µM in the concentration range of 0.1–100 µM. Furthermore, the Co-TCPP(Fe)/rGO/Nafion composite material composed of micron-sized, ultrathin lamellar structures also shows high reusability due to the stability of its coordination structure and can demonstrate good results when applied to the actual sample detection of human urine. Full article

A series of novel fluorescent donor–acceptor–donor (D-A-D) dyes containing [1,2,5]oxadiazolo[3,4-d]pyridazine and its 1-oxide as electron-withdrawing groups has been synthesized and thoroughly investigated using X-ray diffraction and molecular spectroscopy methods. This study showed that the introduction of N-oxide into the 1,2,5-oxadiazole ring in the acceptor fragment leads to a significant decrease in the luminescence intensity and quantum yield of the dyes. A comprehensive comparison of the photophysical properties of the obtained compounds containing the 1,2,5-oxadiazole ring with the previously studied [1,2,5]thia- and 1,2,5-selenadiazolo[3,4-d]pyridazine analogs showed that the oxygen substitution in the acceptor fragment shifts the phosphorescence maximum from the NIR region of 980–1100 nm to the red region of 690–770 nm. In contrast, for oxygen- and sulfur-containing dyes, purely red fluorescence with a maximum in the spectral range of 620–900 nm is observed. The crystal structures of furoxan-containing 3d·½CHCl₃ and furazan-containing 4d exhibit a non-planar [1,2,5]oxadiazolo[3,4-d]pyridazine fragment. We have found that short non-covalent interactions of the furoxan system with a lattice chloroform molecule in 3d lead to luminescence quenching. Meanwhile, in the 4d dye, the intermolecular π-π interactions of pyridazine nitrogen atoms with the N-carbazolyl group of the adjacent molecule should facilitate intermolecular charge transfer (ICT) emission. Thus, the luminescence maxima for these dyes can be tuned across a broad range of 700–1100 nm by varying the number of chalcogen atoms, highlighting the potential for tailoring optical properties in optoelectronic applications. Full article

Lysosomes are important acidic subcellular organelles whose dysfunction can lead to some related diseases. The development of new lysosome-imaging-guided AIEgens for the photodynamic therapy of cancer cells is important. In this work, two novel organic compounds with AIE characteristics, namely, TPAB-CF₃ and TPAB-diCF₃, were designed and synthesized by introducing the weakly basic morpholinyl moiety with lysosome-targeting ability into a triphenylamine-based luminogen. The distorted spatial feature of TPA and the D₁-D₂-π-A structure of these AIEgens prevented the aggregation-caused quenching of traditional fluorescent molecules and efficiently promoted the separation of the HOMO and LUMO. The outcomes were AIE features and a narrow single-triplet energy gap. Furthermore, TPAB-CF₃ and TPAB-diCF₃ showed bright yellow fluorescence emission peaks at 577 and 601 nm; large Stokes shifts of 234 and 256 nm, respectively; and excellent lysosome-targeted imaging of HeLa cells (Pearson’s coefficient = 0.90). In addition to the good ¹O₂-generation ability under light irradiation, these AIEgens achieved the high-efficiency bright lysosome imaging-guided photodynamic killing of cancer cells under white-light irradiation. Full article

The title compound, i.e., (Z)-4-(azulen-1-ylmethylene)-2-phenyloxazol-5(4H)-one (3), has previously been synthesized in a good yield (56%) using the Erlenmeyer–Plöchl procedure. The crystal structure of 3 is described herein along with the results of a Hirshfeld surface analysis. Crystals of compound 3 were obtained through the slow evaporation of a mixture of petroleum ether/dichloromethane = 1:1 (vol.) at room temperature. This compound has a monoclinic system: a P2₁/n space group at room temperature. Its crystal packing is driven by π-π interactions between neighboring molecules in the range of 3.60–3.71 Å and by hydrogen bonds (D-H···A = 2.58 Å). Full article

β-glucuronidase is an important hydrolase, which plays an important role in drug metabolism, clinical diagnostics, and biotransformation. This study focuses on the heterologous expression, isolation, purification, and its enzymatic properties of β-glucuronidase CpGUS from Clostridium perfringens, as well as its application in the whole-cell transformation of unconjugated bilirubin from pig bile. A recombinant E. coli BL21(DE3)/pET-28a-CpGUS was constructed for the heterologous expression of CpGUS, with the majority of the expressed enzyme being soluble. Enzymatic analysis showed that CpGUS displayed optimal activity at pH 5.0 and 45 °C, and it rapidly lost activity at pH < 4.5. Metal ions, such as Mg²⁺ and Fe²⁺, enhanced CpGUS catalysis, while Zn²⁺, K⁺, Fe³⁺, Mn²⁺, Cu²⁺, and Na⁺ inhibited it. Notably, Cu²⁺ and Fe³⁺ can significantly inhibit β-glucuronidase, resulting in the complete loss of its activity. The results of the whole-cell transformation experiment show that when E.coli BL21(DE3)/ pET-28a-CpGUS at an OD₆₀₀ of 10 was incubated at pH 5.0, a temperature of 45 °C, and a rotation speed of 200 rpm for 12 h, the hydrolysis rate of the conjugated bilirubin in pig bile reached 81.1%, the yield of unconjugated bilirubin was 76.8%, and the purity of unconjugated bilirubin was 98.2%. The three-dimensional structure of CpGUS was predicted using AlphaFold2 (AlphaFold v2.0, DeepMind Technologise Limited, London, UK), and p-Nitrophenyl-β-D-Glucuronide (pNPG) and conjugated bilirubin were then docked to the CpGUS protein model using SWISSDOCK. The best docked conformations of the CpGUS–pNPG and CpGUS–conjugated bilirubin complex systems were simulated by independent 500 ns molecular dynamics (MD) runs with the RSFF2C force field, and the binding dynamic and catalytic mechanism of each system were obtained. The results indicated that π-π stacking, hydrogen bonding, and hydrophobic interactions between the key residue Tyr472 and the benzene ring of pNPG molecules are crucial for its catalytic process. Similarly, for the binding and catalysis of conjugated bilirubin by CpGUS, the π-π stacking and hydrogen bonding and hydrophobic interactions between the sidechains of residues Phe368 and Tyr472 and the benzene ring of conjugated bilirubin play a synergistic role during its catalytic process. Their total binding free energy (∆G_bind) values were calculated to be as high as −65.05 ± 12.66 and −86.70 ± 17.18 kJ/mol, respectively. These results suggest that CpGUS possesses high binding and catalytic hydrolysis properties for both pNPG and conjugated bilirubin. Full article

The [2 + 2] cycloaddition reactions of the heterocumulene (N=C=N) with the heavy imine-like molecule Ge=G15-Rea (G15 = Group 15 element) were examined using density functional theory (M06-2X-D3/def2-TZVP). The theoretical findings indicate that the doubly bonded Ge=G15 moiety in Ge=G15-Rea (L₁L₂Ge=G15L₃) is characterized by electron-sharing bonding between the triplet L₁L₂Ge and triplet G15–L₃ fragments. All five Ge=G15-based heavy imine analogues readily undergo [2 + 2] cycloaddition reactions with N=C=N. Energy decomposition analysis (EDA–NOCV) suggests that the [2 + 2] cycloaddition reaction between Ge=G15-Rea and N=C=N involves a donor–acceptor (singlet–singlet) interaction instead of an electron-sharing (triplet–triplet) interaction. Frontier molecular orbital (FMO) theory and the energy decomposition analysis–natural orbitals for chemical valence (EDA–NOCV) findings emphasize that the key bonding interaction involves the occupied p-π orbital of Ge=G15-Rea and the vacant p-π* orbital of C=N=C. Based on the activation strain model results, the activation barrier of the [2 + 2] cycloaddition reaction is predominantly controlled by the deformation energies of Ge=G15-Rea and N=C=N. Full article

Because of the involvement of π-electron cyclic constituents in their side chains, the so-called aromatic residues give rise to a number of strong, narrow, and well-resolved lines spread over the middle wavenumber (1800–600 cm⁻¹) region of the Raman spectra of peptides and proteins. The number of characteristic aromatic markers increases with the structural complexity (Phe → Tyr → Trp), herein referred to as (F_i = 1, …, 6) in Phe, (Y_i = 1, …, 7) in Tyr, and (W_i = 1, …, 8) in Trp. Herein, we undertake an overview of these markers through the analysis of a representative data base gathered from the most structurally simple tripeptides, Gly-Xxx-Gly (where Xxx = Phe, Tyr, Trp). In this framework, off-resonance Raman spectra obtained from the aqueous samples of these tripeptides were jointly used with the structural and vibrational data collected from the density functional theory (DFT) calculations using the M062X hybrid functional and 6-311++G(d,p) atomic basis set. The conformation dependence of aromatic Raman markers was explored upon a representative set of 75 conformers, having five different backbone secondary structures (i.e., β-strand, polyproline-II, helix, classic, and inverse γ-turn), and plausible side chain rotamers. The hydration effects were considered upon using both implicit (polarizable solvent continuum) and explicit (minimal number of 5–7 water molecules) models. Raman spectra were calculated through a multiconformational approach based on the thermal (Boltzmann) average of the spectra arising from all calculated conformers. A subsequent discussion highlights the conformational landscape of conformers and the wavenumber dispersion of aromatic Raman markers. In particular, a new interpretation was proposed for the characteristic Raman doublets arising from Tyr (~850–830 cm⁻¹) and Trp (~1360–1340 cm⁻¹), definitely excluding the previously suggested Fermi-resonance-based assignment of these markers through the consideration of the interactions between the aromatic side chain and its adjacent peptide bonds. 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

Silver (Ag) is a precious and valuable metal, and it has many carrier minerals. Through LA-ICP-MS analysis, it was found that jamesonite not only contains lead (Pb) and antimony (Sb) as precious metals but also trace amounts of Ag. In practice, the flotation method is generally used to recover these metals. This paper employs density functional theory calculations to demonstrate that after Ag doping in jamesonite, the Ag atoms exist in the lattice channels of jamesonite, and they form strong covalent bonds with the S atoms, resulting in strong interactions. When Ag is doped in the channels, the adsorption of sodium diethyldithiocarbamate (DDTC) as a collector on the Ag-doped jamesonite surface is the strongest, while that of butyl xanthate is the weakest. The adsorption interactions on the Ag-doped jamesonite surface are also stronger than on pure jamesonite. Coordination chemistry studies reveal that Ag⁺ undergoes a transition from a d¹⁰ to a d⁹s¹ electronic configuration when incorporated into jamesonite, which increases its reactivity by generating unpaired electrons available for π-backbonding with collector molecules. Furthermore, owing to the high polarizability of Ag, the presence of Ag atoms alters the electronic environment of the surrounding Pb atoms, which enhances the π-backbonding interactions between the adsorbate reagent molecules and the Ag active sites. The research results are of great significance for the efficient recovery of Ag-containing jamesonite and provide a reference for the study of the properties of Ag-doped minerals. Full article