Structural Chemistry最新文献_第10页

Theoretical study of the ESIPT mechanism of 2-(Benzothiazol-2-yl)-5-bromophenol(BBS-OH) and its derivatives 2-（苯并噻唑-2-基）-5-溴苯酚（BBS-OH）及其衍生物的ESIPT机理的理论研究

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-06-04 DOI: 10.1007/s11224-025-02500-y

Changyu Wang, Menghan Ma, Fulin You, Qiang Liu, Yi Wang, Yingmin Hou

引用次数: 0

Synthesis, structure, Hirshfeld surface analysis, molecular docking, and molecular dynamic studies of two carbendazim salts 两种多菌灵盐的合成、结构、Hirshfeld表面分析、分子对接和分子动力学研究

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-06-04 DOI: 10.1007/s11224-025-02515-5

Zebo Azatovna Boltayeva, Bakhtiyar Tulyaganovich Ibragimov, Alisher Gulumbayevich Eshimbetov, Jamshid Mengnorovich Ashurov, Abror Khamidjanovich Ruzmetov, Adkhamjon Sadullayevich Normamatov, Yuldosh Yusupboyevich Yakubov, Khayit Khudaynazarovich Turaev, Manzura Ilxomovna Olimova, Duncan H. Gregory, Ikram Iskandarovich Abdullaev, Abul Monsur Showkot Hossain, Aziz Bakhtiyarovich Ibragimov

{"title":"Synthesis, structure, Hirshfeld surface analysis, molecular docking, and molecular dynamic studies of two carbendazim salts","authors":"Zebo Azatovna Boltayeva, Bakhtiyar Tulyaganovich Ibragimov, Alisher Gulumbayevich Eshimbetov, Jamshid Mengnorovich Ashurov, Abror Khamidjanovich Ruzmetov, Adkhamjon Sadullayevich Normamatov, Yuldosh Yusupboyevich Yakubov, Khayit Khudaynazarovich Turaev, Manzura Ilxomovna Olimova, Duncan H. Gregory, Ikram Iskandarovich Abdullaev, Abul Monsur Showkot Hossain, Aziz Bakhtiyarovich Ibragimov","doi":"10.1007/s11224-025-02515-5","DOIUrl":"10.1007/s11224-025-02515-5","url":null,"abstract":"<div>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.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 1","pages":"259 - 272"},"PeriodicalIF":2.2,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043489","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}

引用次数: 0

Structural and electronic properties of novel diazahomoadamantane-based hydrazones: synthesis, characterization, and DFT insights 新型重氮异质金刚烷基腙的结构和电子性质：合成、表征和DFT见解

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-06-03 DOI: 10.1007/s11224-025-02517-3

Bshair Ali Sadeq, Rahman Tama Alasadi, Sajid Hassan Guzar

引用次数: 0

Theoretical and experimental study on a new spiro compound 3-(2-(2-hydroxyphenyl)hydrazono)-1,5-dioxaspiro[5.5]undecane-2,4-dione 新型螺旋化合物3-（2-（2-羟基苯基）腙）-1,5-二氧螺旋[5.5]十一烷-2,4-二酮的理论与实验研究

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-06-03 DOI: 10.1007/s11224-025-02525-3

Yunju Zhang, Xia Wang, Wulan Zeng

引用次数: 0

DFT-based evaluation of C3N2 nanosheet as sensor against industrial gaseous effluents: NH3, NCl3, NF3, COCl2, and SOCl2 基于dft的C3N2纳米片对工业废气NH3、NCl3、NF3、COCl2和SOCl2传感器的评价

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-06-01 DOI: 10.1007/s11224-025-02499-2

Kinza Hanif, Riaz Hussain, Kiran Lal, Muhammad Durair Sajjad Haider, Ajaz Hussain, Khaled Fahmi Fawy, Khurshid Ayub

{"title":"DFT-based evaluation of C3N2 nanosheet as sensor against industrial gaseous effluents: NH3, NCl3, NF3, COCl2, and SOCl2","authors":"Kinza Hanif, Riaz Hussain, Kiran Lal, Muhammad Durair Sajjad Haider, Ajaz Hussain, Khaled Fahmi Fawy, Khurshid Ayub","doi":"10.1007/s11224-025-02499-2","DOIUrl":"10.1007/s11224-025-02499-2","url":null,"abstract":"<div>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 (EHOMO-ELUMO) 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.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 1","pages":"209 - 226"},"PeriodicalIF":2.2,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043452","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}

引用次数: 0

Structural and energetic evaluation of boron carbide (B₁₆C₁₆) nanocage as a sensing material for A-series nerve agents: a DFT study 碳化硼（B₁₆C₁₆）纳米笼作为a系列神经毒剂传感材料的结构和能量评价：DFT研究

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-05-30 DOI: 10.1007/s11224-025-02522-6

Nora Hamad Al-Shaalan, Hafiz Ali Rizwan, Muhammad Usman Khan, Abida Anwar, Minahil Ishtiaq, Mohammed A. Amin

{"title":"Structural and energetic evaluation of boron carbide (B₁₆C₁₆) nanocage as a sensing material for A-series nerve agents: a DFT study","authors":"Nora Hamad Al-Shaalan, Hafiz Ali Rizwan, Muhammad Usman Khan, Abida Anwar, Minahil Ishtiaq, Mohammed A. Amin","doi":"10.1007/s11224-025-02522-6","DOIUrl":"10.1007/s11224-025-02522-6","url":null,"abstract":"<div>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 (EFL) 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.<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 1","pages":"185 - 207"},"PeriodicalIF":2.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043428","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}

引用次数: 0

New bis-azido iron(III) meso-arylporphyrin complex: spectroscopic characterization, solid state molecular structure, DFT, MEP, QTAIM calculations and Hirshfeld surface analyses 新型双叠氮铁（III）介芳基卟啉配合物：光谱表征、固态分子结构、DFT、MEP、QTAIM计算和Hirshfeld表面分析

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-05-29 DOI: 10.1007/s11224-025-02526-2

Mondher Dhifet, Hayder Mohamed, Nabil Benzerroug, Houcine Ghalla, Ghayth Rigane, Ridha Ben Salem

{"title":"New bis-azido iron(III) meso-arylporphyrin complex: spectroscopic characterization, solid state molecular structure, DFT, MEP, QTAIM calculations and Hirshfeld surface analyses","authors":"Mondher Dhifet, Hayder Mohamed, Nabil Benzerroug, Houcine Ghalla, Ghayth Rigane, Ridha Ben Salem","doi":"10.1007/s11224-025-02526-2","DOIUrl":"10.1007/s11224-025-02526-2","url":null,"abstract":"<div>Herein, our research team presented an iron(III) hexa-coordinated porphyrin complex (I) having the formula [Na(18-C-6)(H2O)2][FeIII(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.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 1","pages":"165 - 184"},"PeriodicalIF":2.2,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043459","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}

引用次数: 0

Structures and properties of M2Cn (M = Be, Mg; n = 8–20) clusters M2Cn （M = Be, Mg; n = 8-20）簇的结构与性能

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-05-27 DOI: 10.1007/s11224-025-02519-1

Shuang Long Jiang, Qi Liang Lu, Qi Quan Luo

{"title":"Structures and properties of M2Cn (M = Be, Mg; n = 8–20) clusters","authors":"Shuang Long Jiang, Qi Liang Lu, Qi Quan Luo","doi":"10.1007/s11224-025-02519-1","DOIUrl":"10.1007/s11224-025-02519-1","url":null,"abstract":"<div>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 M2Cn (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. Be2Cn 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 M2Cn 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.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 1","pages":"149 - 164"},"PeriodicalIF":2.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043458","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}

引用次数: 0

Exploring the Cys62–Cys69 disulfide bridge in human thioredoxin: insights from quantum mechanics and molecular dynamics simulations 探索人体硫氧还蛋白中的Cys62-Cys69二硫桥：来自量子力学和分子动力学模拟的见解

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-05-27 DOI: 10.1007/s11224-025-02518-2

Lina Ould Mohamed, Soraya Abtouche, Xavier Assfeld

{"title":"Exploring the Cys62–Cys69 disulfide bridge in human thioredoxin: insights from quantum mechanics and molecular dynamics simulations","authors":"Lina Ould Mohamed, Soraya Abtouche, Xavier Assfeld","doi":"10.1007/s11224-025-02518-2","DOIUrl":"10.1007/s11224-025-02518-2","url":null,"abstract":"<div>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.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 1","pages":"135 - 147"},"PeriodicalIF":2.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043379","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}

引用次数: 0

Mechanistic study of the [2 + 2] cycloaddition of ethylene with ketene derivatives via MEDT 乙烯与烯酮衍生物[2 + 2]环加成的机理研究

IF 2.2 4区化学

Structural Chemistry Pub Date : 2025-05-27 DOI: 10.1007/s11224-025-02520-8

Mohamed Chellegui, Ines Salhi, Ali Ben Ahmed, Sofiane Benmetir, Raad Nasrullah Salih, Haydar A. Mohammad-Salim, Jesus Vicente de Julián-Ortiz

{"title":"Mechanistic study of the [2 + 2] cycloaddition of ethylene with ketene derivatives via MEDT","authors":"Mohamed Chellegui, Ines Salhi, Ali Ben Ahmed, Sofiane Benmetir, Raad Nasrullah Salih, Haydar A. Mohammad-Salim, Jesus Vicente de Julián-Ortiz","doi":"10.1007/s11224-025-02520-8","DOIUrl":"10.1007/s11224-025-02520-8","url":null,"abstract":"<div>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.</div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 1","pages":"111 - 124"},"PeriodicalIF":2.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043456","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}

引用次数: 0