Structural Chemistry最新文献

{"title":"A DFT modeling of the effect of CH/N and CH/P exchanges on tandem Cope rearrangement and [2+2] cycloaddition of cis-1,2-diethylnylcyclopropane and its mono-hetero analogues","authors":"Ayushi Shekhawat,&nbsp;Raj K. Bansal","doi":"10.1007/s11224-025-02679-0","DOIUrl":"10.1007/s11224-025-02679-0","url":null,"abstract":"<div><p>The effect of mono- and di-substitution of the terminal –C ≡ CH groups of <i>cis</i>-1,2<b>-</b>diethynylcyclopropane with CH/N or CH/P moieties has been theoretically investigated at the DFT (B3LYP/6–31 +G(d)) level. On substitution of one or both CH groups with phosphorus atoms, there is remarkable decrease in the activation free energy barriers (ΔG^#) for both reaction steps and the overall process becomes exergonic. In contrast, on similar substitution with the nitrogen atom, there is distinct increase in the ΔG^# values and both reactions turn endergonic. These opposing trends could be rationalized on the basis of the relative strengths of the C≡ P and C ≡ N bonds, the former being significantly weaker than the latter. The effect of replacing CH₂ group in the cyclopropane ring with heteroatoms (NH or PH) was also investigated at the same theoretical level, when broadly similar trends were observed.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2557 - 2565"},"PeriodicalIF":2.3,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950515","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the bond angle variations in XH(_3) [X = N, P, As, Sb]","authors":"Alberto Guerra-Barroso,&nbsp;Tanmoy Mondal,&nbsp;António J. C. Varandas","doi":"10.1007/s11224-025-02672-7","DOIUrl":"10.1007/s11224-025-02672-7","url":null,"abstract":"<div><p>Attempts are made to unravel the ground state H-X-H bond angles in group-15 hydrides (XH<span>(_3)</span>, where X=N, P, As and Sb) via high level quantum chemical calculations. The energy differences between s and p valence orbitals of the central atoms and their linear combinations demonstrate a systematic increase of p and decrease of s orbital character in the involved hybrid orbital as one descends through group-15. This parameter quantitatively indicates the deterioration of s-p orbital overlapping and reveals a systematic decrease in the H-X-H angles from NH<span>(_3)</span> to SbH<span>(_3)</span>, and thus corroborates the existing experimental observations.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 1","pages":"125 - 134"},"PeriodicalIF":2.2,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An in-silico investigation of 8-hydroxyquinoline (8-HoQ) derivatives as potential anti-tuberculosis agents by targeting glutamate kinase","authors":"Malathi Marimuthu,&nbsp;Selvakumar Balasubramanian,&nbsp;Ramanan Balasubramanian Viswanathan,&nbsp;Hari Prasad Parthiban,&nbsp;Malathi Mahalingam,&nbsp;Gayathri Kasirajan","doi":"10.1007/s11224-025-02677-2","DOIUrl":"10.1007/s11224-025-02677-2","url":null,"abstract":"<div>\u0000 \u0000 <p>The current study has detailed the computational methodologies to assess the therapeutic potential of carbonyl-substituted derivatives <b>1</b>–<b>4</b> of 8-hydroxyquinoline (8-HoQ). Various computational techniques, including density functional theory, global chemical descriptors and molecular docking, were applied to analyze the properties of the 8-HoQ derivatives and the interactions between them and target proteins. Molecular stability and reactivity were evaluated using frontier molecular orbital (FMO) and molecular electrostatic potential studies, while topological visualizations, such as electron localization function, localized orbital locator, reduced density gradient, and interaction region indicator, provided insights into molecular polar charge characteristics. Molecular reactive sites identified from these analyzes were utilized in molecular docking studies targeting Glutamate Kinase (GK), a previously untapped enzyme in tuberculosis treatment. The 8-HoQ derivatives <b>1</b>–<b>4</b> exhibited binding affinity of -6.8, -7.5, -7.2, and − 8.2 kcal mol⁻¹, respectively, which are higher than the standard ligand of L-Glutamic acid, demonstrating their potential as GK activators to inhibit <i>Mycobacterium tuberculosis</i> (mtb). The high binding score derivative 8HoQ derivative 4 was subjected to a 100 ns molecular dynamics simulation, to confirm the structural stability and compactness of the GK–ligand complex. The FMO-derived molecular descriptors revealed an increase in hydrophilic nature and strong protein-binding affinities with respect to the position of carbonyl functional group substitutions. These findings, corroborated by molecular docking and in silico Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) profiling, indicate high intestinal absorption and suggest that suitable functional substitution in the quinoline ring makes promising candidates within the 8-HoQ system for evaluating pharmacological suitability.</p>\u0000 </div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2519 - 2539"},"PeriodicalIF":2.3,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A simple exercise of structure correlation to investigate tetrachlorocuprate geometric preferences and discuss data mining literacy","authors":"Alessia Bacchi","doi":"10.1007/s11224-025-02674-5","DOIUrl":"10.1007/s11224-025-02674-5","url":null,"abstract":"<div>\u0000 \u0000 <p>This study explores the coordination geometry of tetrachlorocuprate(II) anions (CuCl₄²⁻) in the solid state using data mining techniques applied to crystallographic databases. By analyzing over 800 crystal structures from the Cambridge Structural Database, the research reveals that the commonly assumed square planar and tetrahedral geometries are underrepresented. Instead, a disphenoidal (flattened tetrahedral) geometry emerges as the predominant configuration. Principal Component Analysis (PCA) of six Cl–Cu–Cl bond angles confirms a continuous deformation pathway between idealized geometries, mapping a pseudorotation. Comparative studies with related halocuprates and other metal ions (Ni²⁺, Zn²⁺) further support the influence of electronic configuration and ligand repulsion on geometry preferences. The work also serves as an educational case study, demonstrating how database searches and statistical tools can enhance structural chemistry literacy and prepare future researchers for intelligent use of Artificial Intelligence (AI) in chemical data analysis.</p>\u0000 </div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 3","pages":"1079 - 1088"},"PeriodicalIF":2.2,"publicationDate":"2025-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s11224-025-02674-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147938689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational insights into γ-M₂O₃-Based nanocarriers for paracetamol: surface reactivity and interaction mechanisms","authors":"Faeq A. Al-Temimei","doi":"10.1007/s11224-025-02660-x","DOIUrl":"10.1007/s11224-025-02660-x","url":null,"abstract":"<div><p>The potential of γ-M₂O₃-based nanoparticles (M = Fe, Al, Ni, Rh, Ru) as carriers for paracetamol (PCT) was investigated using DFT at the M06-2X level. Geometry optimizations confirmed stable structures, with adsorption energies ranging from − 1.20 to − 1.85 eV, indicating favorable non-covalent interactions. PCT adsorption notably increased dipole moments (γ-Ni₂O₃: 3.950 → 7.929 D; γ-Al₂O₃: 1.409 → 7.290 D), expanded molecular volumes (~ 604–607 → ~803–807 ų), and reduced densities, reflecting structural adaptation upon drug binding. Surface potential, charge separation, and molecular polarity index rose significantly for γ-Ni₂O₃@PCT (26972 kcal/mol, 2600.82 kcal/mol, 1169.62 eV), promoting stronger interactions with the drug. MEP maps revealed electrophilic sites on O/N atoms and nucleophilic regions on metals/H, supporting heterogeneous charge distribution and favorable binding. RDG analysis showed highest reactive densities for Ni- and Ru-substituted surfaces, while QTAIM confirmed mainly weak, electrostatic interactions with van der Waals forces and localized hydrogen bonds (electron densities at BCPs: 0.10–0.21 Å⁻³). These results indicate that metal substitution, particularly with Ni, enhances electronic properties and adsorption capability, making γ-Ni₂O₃@PCT a promising and stable nanocarrier platform for paracetamol delivery.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2505 - 2517"},"PeriodicalIF":2.3,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computation and experimental investigation of halogenated 2,3-dihydrobenzo[b][1,4]thiazepine: XRD, DFT and NCIanalysis","authors":"Marole M. Maluleka,&nbsp;Vusi G. Mbazima","doi":"10.1007/s11224-025-02665-6","DOIUrl":"10.1007/s11224-025-02665-6","url":null,"abstract":"<div><p>The synthesis of halogenated 2,3-dihydrobenzo[<i>b</i>] [1,4]thiazepines from chalcones was achieved using 2-aminothiophenol in acidic conditions. The structure of the resulting 2,3-dihydrobenzo[<i>b</i>] [1,4]thiazepine derivatives was determined using ¹H-NMR, ¹³C-NMR, IR, and mass spectrometry techniques. The stereochemistry of these molecular hybrids was clearly determined through single-crystal X-ray diffraction techniques, supplemented by density functional theory methods. Halogen bonds are identified in the solid-state structure of <b>2b</b>, attributed to C-I···Br Type II halogen interactions. Hirshfeld surface analysis, three-dimensional fingerprints, the energy framework, and molecular electrostatic potentials were employed to assess these interactions. The NCI–RDG and QTAIM analysis were conducted to examine noncovalent interactions.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2491 - 2503"},"PeriodicalIF":2.3,"publicationDate":"2025-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanism of ethane decomposition over Au. A combined DFT study and kinetics modeling","authors":"Vinícius Martinelli,&nbsp;Rodrigo M. Pontes","doi":"10.1007/s11224-025-02670-9","DOIUrl":"10.1007/s11224-025-02670-9","url":null,"abstract":"<div><p>C-H bond activation in light alkanes figures among the most important industrial processes in our days. Of particular interest is ethane dehydrogenation to generate ethylene, a chemical precursor for the preparation of a number of commercially interesting compounds. In the present work, we investigate the ethane dehydrogenation to ethylene catalyzed by Au, as represented by an Au₈ cluster. The double-hybrid DFT functional DSD-PBEP86 was used to obtain the intermediates and transition states for some competitive reaction paths. The two most important of these pathways were used to structure a set of kinetic rate equations from which the concentration of each intermediate throughout the reaction was obtained. The model equations allowed us to determine under which conditions each product, i.e. CH₄ or CH₂CH₂, is favored. Under high hydrogen availability, CH₄ is the main product. When the only source of hydrogen is the dehydrogenation of CH₃CH₃ itself, H atoms over Au should be rare and CH₂CH₂ is expected to be predominant. Finally, we used a combination of wave function analysis techniques in order to give a chemical interpretation for the relative activation energies in the main steps involved in each of the two competing routes.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2467 - 2480"},"PeriodicalIF":2.3,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational insights into π-spacer integration for reduced energy loss in symmetric A-π-D-π-A NF-OSCs","authors":"Muneeba Liaquat,&nbsp;Riaz Hussain,&nbsp;Muhammad Durair Sajjad Haider,&nbsp;Javeria Saeed,&nbsp;Ajaz Hussain,&nbsp;Khurshid Ayub,&nbsp;Saleh S. Alarfaji","doi":"10.1007/s11224-025-02669-2","DOIUrl":"10.1007/s11224-025-02669-2","url":null,"abstract":"<div><p>This study explores enhancing organic solar cells (OSCs) by adding π-spacers to a novel non-fullerene acceptor (DC-IDT2Tz, A-π–D–π-A framework). Five derivatives (<b>M1–M5</b>) were designed and analyzed using DFT/TD-DFT at B3LYP/6-31G (d, p) level. The geometries were optimized in the gas phase, while the absorption spectra and excited-state properties were calculated using the CPCM solvation model in chloroform. All modified molecules showed improved optoelectronic properties, leading to reduced energy loss, with <b>M2</b> and <b>M4</b> exhibiting greater planarity, and <b>M2</b> achieving the highest λ_max (841.53 nm). Reduced density gradient (RDG)/non-covalent interaction (NCI) analyses confirmed stability and favorable interactions. In contrast, the transition density matrix (TDM), electron/hole overlap, and charge density difference (CDD) indicated efficient charge transfer, especially in <b>M1</b>, <b>M2</b>, and <b>M4</b>. <b>M1</b> and <b>M2</b> showed low reorganization energies and enhanced charge mobility. Photovoltaic simulations revealed <b>M2</b> had the highest open circuit voltage (V_OC) (2.1067 V), fill factor (0.9344), light harvesting efficiency (0.9974), E_loss (0.0162 eV), and predicted J_sc, suggesting superior PCE and reduced energy loss. <b>M2:PTB7-Th</b> complex studies confirmed effective interfacial charge separation. Overall, <b>M1–M5</b>, especially <b>M2</b>, are promising candidates for high-performance, eco-friendly OSCs.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2443 - 2465"},"PeriodicalIF":2.3,"publicationDate":"2025-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis, structural features, computational study along with molecular docking examination of organosulfur mercaptoacetic acid based compound","authors":"Sabiya Osmanova,&nbsp;Malahat Kurbanova,&nbsp;Muhammad Ashfaq,&nbsp;Mehran Feizi-Dehnayebi,&nbsp;Muhammad Nawaz Tahir,&nbsp;Onur Şahin","doi":"10.1007/s11224-025-02668-3","DOIUrl":"10.1007/s11224-025-02668-3","url":null,"abstract":"<div><p>We carried out a thiylating reaction of p-nitroacetophenone with thioglycolic acid. The reaction was carried out in a benzene solution, with a molar ratio of the initial components of 1:4. 1,1-bis-(carboxymethylthio)-1-p-nitrophenylethane (CTNE). Structural features are evaluated via Fourier transform infrared (FT-IR) spectroscopy, ¹H NMR and single crystal X-ray diffraction (XRD) analysis. Structure is composed of an organosulfur molecule and a water molecule. Organosulfur molecule adopted non-planar conformation supported via dihedral angle of 71.3 (4)° among carboxylic acid groups. Supramolecular organization is primarily supported via O-H⋯O bonding. Further stability of the supramolecular organization is due to π⋯π interactions with inter-centroid separation range from 3.85 to 4.01 Å. Strong and weaker interactions are evaluated via Hirshfeld surface analysis which showed that H⋯O contact has highest contribution in stability of the supramolecular organization. DFT calculations at the B3PW91/6-311 + + g (2d,2p) level was employed to optimize the molecular geometry and assess the electronic properties of the synthesized compound. Highest Occupied Molecular Orbital (HOMO)– Lowest Unoccupied Molecular Orbital (LUMO) energy gap (∆E = 4.06 eV) of the synthesized compound indicates enhanced chemical reactivity and biological potential compared to precursor molecules. Furthermore, molecular docking studies demonstrated a promising binding affinity (-7.05 kcal/mol) toward VEGFR2, stabilized through hydrogen bonding and hydrophobic interactions, suggesting potential anticancer activity through angiogenesis inhibition.</p><h3>Graphical Abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2427 - 2441"},"PeriodicalIF":2.3,"publicationDate":"2025-11-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Crystal and molecular structures of benzoylpyrenes and acetylpyrenes. E-, Z-, M- & P-stereodescriptors","authors":"Shmuel Cohen,&nbsp;Benny Bogoslavsky,&nbsp;Tahani Mala’bi,&nbsp;Hannah Daniel Kraus,&nbsp;Israel Agranat","doi":"10.1007/s11224-025-02664-7","DOIUrl":"10.1007/s11224-025-02664-7","url":null,"abstract":"<div><p>The crystal and molecular structures of the following acetylpyrenes (<b>AcPYs</b> ), and benzoylpyrenes (<b>BzPYs</b>) have been determined by X-ray crystallography: 1-acetylpyrene, 2-acetylpyrene, 1,3-diacetylpyrene, 1,6-diacetylpyrene, 1,8-diacetylpyrene, 2,7-diacetylpyrene, 1-benzoylpyrene <b>(1-BzPY)</b>, 1,3-dibenzoylpyrene, 1,6-dibenzoylpyrene, 1,8-dibenzoylpyrene (<b>1</b>,<b>8-Bz</b>_<b>2</b><b>PY</b>), 1-(4-fluorobenzoyl)pyrene, and 1,6-bis(4’-fluorobenzoyl)pyrene <b>.</b> Special attention was drawn to the stereodescriptors <i>E</i>,<i> Z</i>,<i> P</i> and <i>M</i> in the conformations of <b>AcPYs</b> and <b>BzPYs</b>. Geometrical parameters of the molecular structures of the <b>AcPYs</b> and <b>BzPYs</b>. and of previously reported crystal structures, including 1,3,6-tribenzoylpyrene and 1,3,6,8-tetrabenzoylpyrene are provided. Two cases of crystal dynamic isomerism, as distinct from polymorphism, have been revealed: <b>1</b><b><i>E</i></b><b><i>-BzPY</i></b>/<b>1</b>/<b><i>Z</i></b><b><i>-BzPY</i></b> and <b>1</b><b><i>Z</i></b><b>8</b><b><i>E</i></b><b>-Bz</b>_<b>2</b><b>PY</b>/<b>1</b><b><i>Z</i></b><b>8</b><b><i>Z</i></b><b>-Bz</b>_<b>2</b><b>PY</b>. Most of the crystal structures of <b>AcPYs</b> and <b>BzPYs</b> under study adopt the more stable <i>Z</i>-conformations of the acetyl and benzoyl groups vis-à-vis the pyrene ring. The deviation from planarity of the carbonyl groups from the plane of the pyrene ring system is higher in <b>AcPYs</b>, as compared with <b>BzPYs.</b> The rich stereochemistry of the crystal structures of acetylpyrenes and benzoylpyrenes, as manifested in the <i>E</i>-, <i>Z</i>-, <i>M</i>- and <i>P</i>-stereodescriptors is noted.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 1","pages":"9 - 23"},"PeriodicalIF":2.2,"publicationDate":"2025-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s11224-025-02664-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043494","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}