Structural Chemistry最新文献

In this work, the excited state intramolecular proton transfer (ESIPT) mechanism of BBS-OH (2-(Benzothiazol-2-yl)-5-bromophenol) and the influence of atomic electronegativity on the ESIPT behavior of BBS-OH molecules and its derivatives have been theoretically explored. By analyzing infrared vibrational spectra, bond lengths and bond angles, the hydrogen bond is strengthened in the S₁ state, as the atom electronegativity decreases, which is further confirmed by the density gradient function (RDG) isosurfaces and scatterplots. The decrease in electronegativity reduces the energy gap, leading to a slight redshift in both absorption and fluorescence spectra. Additionally, potential energy curves (PECs) analysis confirms the ESIPT process can be effectively modulated by tuning atomic electronegativity.

Two carbendazim (CBDZ) salts, (C₉H₁₀N₃O₂)₂SO₄·2H₂O (compound 1) and (C₉H₁₀N₃O₃)·NO₃ (compound 2), have been prepared and characterized using spectroscopic techniques. The crystal structures of both compounds have been solved by single-crystal X-ray diffraction. In both salts, the protonation of CBDZ occurs at the nitrogen atom of the imidazole ring. Hirshfeld surface analysis was conducted to evaluate the nature of the intermolecular interactions in each compound, revealing that O···H/H···O interactions are the dominant components of the resulting 2D fingerprint plots for both compounds. Molecular docking and molecular dynamic studies demonstrated that the protonated form of CBDZ (CBDZH) binds strongly to amino acid residues through hydrogen bonds, van der Waals interactions, and cation (anion)-π interactions, in contrast to neutral CBDZ. The binding affinity for CBDZH (− 29.03/ − 22.52) was found to be approximately three times higher than that of CBDZ (− 11.88/ − 7.19) according to the MMGBSA and MMPBSA methods. Total decomposition analysis indicates a higher contribution of van der Waals and electrostatic energies to the ligand–protein interaction energies with certain amino acid residues for both complexes.

A series of hydrazone derivatives of diazatricyclo[4.3.1.1³,⁸]undecane (3a–3d) were synthesized and characterized spectroscopically. DFT calculations at the B3LYP/6-311G(d,p) level showed that compound 3c had the smallest HOMO–LUMO gap (0.027 eV), indicating high electronic reactivity and suitability for optoelectronic applications, while 3d exhibited the largest gap (0.134 eV), suggesting high chemical stability. MEP and Mulliken analyses confirmed strong nucleophilic sites in 3a and 3c, with 3d displaying a balanced charge distribution. UV–Vis spectra revealed extended conjugation in 3c with absorption near 1100 nm. Thermodynamic analysis ranked 3b as the most stable and energy-efficient compound. These findings support the potential of these molecules in optical and electronic materials development.

The molecular structure and spectral characteristics (FT-IR and UV–Vis) of the new spiro compound, 3-(2-(2-hydroxyphenyl)hydrazono)-1,5-dioxaspiro[5.5]undecane-2,4-dione (HD), were computed using DFT/B3LYP/6-31G(d, p) and compared to experimental spectra. A single-crystal XRD study revealed that the HD molecule was linked by O5 − H5A··O1 intermolecular interactions. The band gap of HOMO–LUMO energy estimates ranged between − 5.936 and − 2.222 eV. The large gap energy (3.714 eV) of HD implied that the molecule had higher stability. MEP surface analysis gave its nucleophilic and electrophilic attack sites. Natural bond orbital (NBO) study revealed the kind and direction of charge transfer, as well as the stabilization energies of HD. Hirshfeld surface analysis was utilized to explain that H···H interaction makes up the majority (45.8%) in HD. Finally, the HD molecule was confirmed to be stable up to 154 ℃ using TG/DSC.

This study explores the potential of C₃N₂ nanosheets as a gas sensor for detecting harmful industrial gases like NH₃, NCl₃, NF₃, COCl₂, and SOCl₂ using DFT computations. The interaction and adsorption of these gases on the C₃N₂ surface were analyzed using methods such as frontier molecular orbitals (FMO), natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM), and electron density difference (EDD). The interaction energies ranged from − 17.37 to − 9.04 kcal/mole, with SOCl₂ showing the highest interaction energy. The charge transfer and (E_HOMO-E_LUMO) energy gaps were slightly reduced for NH₃ and COCl₂, suggesting effective sensing capability. The QTAIM analysis confirmed non-covalent interactions between the gases and the C₃N₂ surface. Overall, the results demonstrate that C₃N₂ nanosheet is more sensitive for detecting and trapping NH₃ and COCl₂.

The presence of chemical nerve agents (CNAs) poses significant threats to both living beings and the environment, making their rapid detection and elimination crucial. In this study, the potential of boron carbide (B₁₆C₁₆) nanocage (BCN) as an electrochemical sensor material for A-series chemical nerve agents (CNAs) was investigated using density functional theory (DFT). The adsorption studies reveal the chemisorption nature of interactions between CNAs and BCN, characterized by high negative adsorption energies for A230@SiteC (-95.136 kcal/mol), A232@SiteA (-31.792 kcal/mol), and A234@SiteB (-92.963 kcal/mol). FMO studies reveal that the energy gaps of 1.40 eV for A230@SiteC, 1.61 eV for A232@SiteC, and 1.46 eV for A234@SiteB decreased from 1.80 eV of pristine BCN. The Fermi level energy (E_FL) undergoes significant shifts in all systems, depending on the density of states (DOS). Topological analyses, including QTAIM and NCI, indicate that the interactions are predominantly of weak covalent or van der Waals nature. The adsorption of CNAs significantly enhances the electrical properties, with electrical conductivity (σ) increasing to 5.98 × 10¹² S/m (A-230@SiteC), 5.73 × 10¹² S/m (A-232@SiteC), and 5.92 × 10¹² S/m (A-234@SiteB). The decrease of work function ((phi)) and short recovery times (τ) in these configurations increases the sensing response (S) 0.0823 for A-230@SiteC, 0.0376 for A-232@SiteC, and 0.0705 for A-234@SiteB. These results highlight the efficiency of BCN as a robust sensor for CNAs, making it a promising candidate for future advancements in chemical sensing technologies.

Graphical abstract

Herein, our research team presented an iron(III) hexa-coordinated porphyrin complex (I) having the formula [Na(18-C-6)(H₂O)₂][Fe^III(TMPP)(N₃)₂] (where TMPP represents the meso-tetra (para-methoxyphenyl) porphyrinato as well as 18-C-6 remains the crown ether). The synthesis and characterization of these chemical species were performed using ¹H NMR, UV/Vis, FT-IR spectra, and Mössbauer spectroscopies. In order to find the molecular structure related to this complex I, X-ray diffraction has been used. The bis-azido iron(III) meso-arylporphyrin complex was studied by exploring the density functional theory (DFT) at the level of the hybrid meta-GGA functional TPSSh combined with triple-ζ quality basis. The optimized chemical structure aligns well with experimental data. A small HOMO–LUMO gap indicates high reactivity and electron-donating ability. MEP highlights strong Fe–N electrophilic interactions, while QTAIM and NCI-RDG confirm the strong N = N bonds and the presence of several electrostatic interactions complex between groups, which may contribute to the enhanced stability of the compound within the crystal lattice. Hirshfeld surface analysis reveals key intermolecular interactions stabilizing the crystal lattice.

One of the most impressive advances in the field of carbon clusters in recent years is the successful synthesis and characterization of a ring consisting of carbon atoms, named cyclo[n]carbon, on the surface of a crystal. Doping with other atoms can greatly affect the structure and electronic properties of host clusters, and can form endohedral fullerenes, doped graphene, heterogeneous carbon ring, etc. Whether the structures of Be and Mg atom doped carbon clusters are ring-, fullerene- or graphene-like configurations is interesting. In this study, the structures and properties of M₂C_n (M = Be, Mg; n = 8–20) clusters are determined by combining structural search and density functional theory. Structural transition from single- or double-ring structures to planar honeycomb-like structures occurred in M₂C₁₅. Be₂C_n with even numbers for n values have relatively high vertical ionization energy and low electron affinity, and the binding energy of M atoms decrease rapidly when the cluster size n is larger the turning point of structural transition. The highest occupied molecular orbital − lowest unoccupied molecular orbital (HOMO–LUMO) gap of M₂C_n decreases with n value. Moreover, bond length, Mayer bond order, charges on M atoms, and aromaticity are studied. Be₂C₁₅ and Mg₂C₁₅ show remarkable aromatic character, and differences in aromaticity between Be₂C₁₆ and Mg₂C₁₆ are comprehensively analyzed.

Thioredoxin 1 (Trx-1) is a crucial redox protein that maintains cellular redox balance by reducing disulfide bonds in target proteins. This study applies quantum chemistry (QM) and the molecular dynamics-perturbed matrix method (MD-PMM) to investigate the impact of disulfide bridge formation between residues Cys62 and Cys69 in thioredoxin. Although the precise function of this inactive site remains uncertain, we aim to understand how it influences the reduction of the active site Cys32-Cys35. First, we compare the reduction of the two disulfide bridges of thioredoxin by analyzing isolated structures using a QM method. Next, the MD-PMM approach is applied to calculate the first reduction of the active site when the second disulfide bridge is either oxidized or reduced. Finally, molecular dynamics (MD) simulations are employed to analyze the geometry of the active site, as well as the solvent-accessible surface area (SASA), root-mean-square deviation (RMSD), and root-mean-square fluctuation (RMSF) in both redox states of the protein. These analyses assess the potential effect of the non-active disulfide bridge on the active site function. Clinical trial number: not applicable.

In this study, the [2 + 2] cycloaddition reaction between ethylene 1 and ketene 2, along with its chalcogen-substituted derivatives 3–5, leading to the formation of four-membered rings, was investigated within the framework of Molecular Electron Density Theory (MEDT) at the B3LYP-D3/6–311 + + G(d,p) level of theory. The dimerization of ethylene exhibits a high activation Gibbs free energy (ΔG^≠ = 88.0 kcal mol⁻¹), reflecting the nonpolar nature of this reaction, which follows a one-step asynchronous mechanism. The incorporation of chalcogen atoms into the ethylene framework leads to a moderate reduction in activation energy, following the trend ketene (2, X = O) > thioketene (3, X = S) > selenoketene (4, X = Se) > telluroketene (5, X = Te). This decrease in activation energy is accompanied by an increase in the reaction’s polarity, as evidenced by the electrophilicity difference between the reactants and the Global Electron Density Transfer (GEDT) at the transition state. Furthermore, the Bonding Evolution Theory (BET) analysis reveals that the introduction of chalcogen atoms alters the reaction mechanism, shifting from a one-step synchronous to a one-step asynchronous pathway. In this revised mechanism, the C–C bond directly attached to the chalcogen atom forms first, underscoring the significant influence of chalcogen substitution on the electronic and structural evolution of the reaction.