Structural Chemistry最新文献

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.

Two N′-(adamantan-2-ylidene)-substituted benzohydrazide derivatives, namely, N′-(adamantan-2-ylidene)-2,4-dichlorobenzohydrazide (1) and N′-(adamantan-2-ylidene)-3,4,5-trimethoxybenzohydrazide (2), were successfully synthesized and thoroughly characterized. Single-crystal X-ray diffraction analysis revealed that both compounds form robust molecular dimers stabilized by multiple hydrogen bonds, including N–H···O/N and C–H···O/N/Cl/π interactions. In the dichloro-substituted compound, numerous C–H···Cl interactions contribute to the stabilization of various molecular dimers in the solid state. Conversely, the trimethoxy-substituted derivative features numerous C–H···O interactions, which stabilize distinct molecular dimeric arrangements. Furthermore, the dichloro compound exhibits a Cl···Cl halogen bond, while the trimethoxy derivative demonstrates a tetrel bond involving methoxy groups. The energetics of the molecular dimers observed in these structures were analyzed, and the intermolecular interactions were further explored using atoms in molecules theory. Furthermore, in vitro antiproliferative activity, molecular docking, and molecular dynamic simulations were conducted to gain deeper insights into their bioactivity.

This study explores the impact of functionalization strategies on single-walled carbon nanotubes (SWCNTs) for drug delivery applications. It focuses on polyethylene glycol (PEG) and PEG-poly (maleic anhydride-alt-1-octadecene) (PEG-PMHC18) functionalized systems, comparing covalent and non-covalent approaches. The choice of functionalization method significantly influences molecular interactions and drug encapsulation behavior. Molecular dynamic (MD) simulations were conducted to evaluate the stability, drug encapsulation efficiency, and molecular mobility of functionalized SWCNTs. Covalent and non-covalent functionalization strategies using PEG and PEG-PMHC18 were analyzed to assess their effects on drug binding. Covalent functionalization provided strong and stable drug binding, ensuring controlled release, but limited molecular flexibility. PEG-PMHC18 covalent functionalization demonstrated enhanced stability due to increased steric interactions. In contrast, non-covalent functionalization offered greater flexibility, facilitating higher drug mobility and faster release. However, it exhibited weaker initial binding, leading to potential instability. The results also revealed that the type of functionalization and PEG chain length influence drug mobility, with non-covalent systems enabling more movement along the nanotube axis, while covalent systems restricted mobility for sustained release. The findings highlight that covalent functionalization is ideal for prolonged drug release, while non-covalent systems are better suited for rapid delivery. Optimizing these approaches can enhance drug carrier performance, balancing stability, mobility, and release characteristics for various therapeutic needs.

Piperidine derivatives are versatile scaffolds with significant potential in drug design due to their broad range of biological activities. In this study, density functional theory (DFT) and molecular dynamics (MD) simulations were employed to investigate the structural, electronic and biological properties of select piperidine-based compounds (1–8). DFT calculations of all the piperidine analogues (1–8) provided insights into molecular geometry, electronic stability and reactivity, MD simulations (100 ns) in explicit solvent revealed key conformational behaviors and interactions including root-mean-square deviation (RMSD), hydrogen bonding, and solvent-accessible surface area elucidating their molecular interactions in a biological environment. Compounds 2 and 4 were evaluated for their inhibitory potential against α-glucosidase and cholinesterase enzymes providing insight into their inhibitory potential and molecular binding interactions with these targets. This study uniquely correlates the structural stability and flexibility of piperidine derivatives with specific functional groups, offering valuable insights for drug design and supporting further experimental and computational exploration.

Benzothiazole-based fluorescent probes, exhibiting promising optical properties, have been widely developed for the detection of chemical and biological contaminants. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods were employed to investigate the sensing mechanism of NO detection using the ratio fluorescence probe 2-(2,3′,5-trimethyl-[1,1′-biphenyl]-3-yl)benzo[d]thiazole (denoted as TBBT). Moreover, the computed emission energy of TBBT more closely matches the experimental data compared to TBBT-T. Our theoretical results suggest that the luminescence properties of TBBT are not based on the excited state intramolecular proton transfer (ESIPT). Additionally, frontier molecular orbitals (FMOs) and “hole-electron” analysis reveal that TBBT and TBBT-NO show significant intramolecular charge transfer (ICT) characteristics, which further explain the mechanism of action of fluorescent probes.

Professor Alan Mackay died on 24th February 2025, aged 98 This series of recollections covers the period around 1975 when he worked on tiling patterns using pentagons and met with Roger Penrose, the discoverer of the first aperiodic tiling pattern using only two shapes of tiles. The creation of a computer program to draw the Penrose pattern allowed for the derivation of a diffraction pattern showing ten-fold symmetry, preceding the actual discovery of quasi-crystals by Dan Shechtman a few years later.

Musing over half a century of interactions with Alan Mackay, a rich array of thoughts on past occasions emerges—personal as well as professional—some serious, some playful, and some approaching the bizarre. Browsing through a few of these thoughts, I attempt to illustrate some of those aspects of Alan that have demonstrated to me not just his broad, radical intellectual imagination, but also his generosity and humanity, as well as how the environment of the Birkbeck Crystallography Department and his links with J.D. Bernal were instrumental in enabling his fertile mind to flourish.