Structural Chemistry最新文献

{"title":"Intermolecular interactions between bovine serum albumin and nanosized methyl pheophorbide systems based on amphiphilic N-vinylpyrrolidone copolymers: experimental studies and quantum-chemical modeling","authors":"Nina S. Emelyanova,&nbsp;Svetlana V. Kurmaz,&nbsp;Daria A. Poletaeva,&nbsp;Alexandr V. Zhilenkov","doi":"10.1007/s11224-025-02448-z","DOIUrl":"10.1007/s11224-025-02448-z","url":null,"abstract":"<div><p>Mixtures of bovine serum albumin and nanosized systems of the fluorescent dye methyl pheophorbide <i>a</i> based on amphiphilic copolymers of N-vinylpyrrolidone in phosphate-buffered saline were studied using UV/visible spectroscopy and dynamic light scattering. The experimental data obtained indicate the possibility of forming joint structures as a result of adsorption of albumin molecules on polymer particles. The quantum-chemical modeling performed allowed us to propose a structure and estimate the energy of intermolecular bonds of the guest molecule in the resulting nanoscale systems both on the particle surface and in hydrophobic regions. The binding energy of the albumin molecule to the surface of the polymer nanoparticle was estimated and a mechanism for the transition of the methyl pheophorbide molecule from the surface of the nanoparticle to one of the four albumin molecule binding sites found using molecular docking was proposed. Such a transition to the blood protein will facilitate the effective delivery of the active substance to target cells.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1457 - 1474"},"PeriodicalIF":2.2,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145163107","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 relative importance of C–H‧‧‧O, C–H‧‧‧π, π‧‧‧π and S‧‧‧π interactions in the crystal of 3-(phenylsulfinyl)-2H-chromen-2-one","authors":"Provash Joarddar,&nbsp;Goutam Biswas,&nbsp;Atish Dipankar Jana,&nbsp;Sasthi Charan Halder,&nbsp;Sandip Kundu","doi":"10.1007/s11224-025-02467-w","DOIUrl":"10.1007/s11224-025-02467-w","url":null,"abstract":"<div><p>Coumarin-based molecules have found important applications in various fields. Present paper explores the X-ray crystal structure and DFT computational studies of a new coumarin-based molecule 3-(phenylsulfinyl)-2H-chromen-2-one. The molecule assumes an “L”-shaped conformation due to intra-molecualr interaction. Various weak intermolecular interactions like C–H‧‧‧O, C–H‧‧‧π and S‧‧‧π interactions play a role in the crystal packing. The present paper explores the relative importance of C–H‧‧‧O, C–H‧‧‧π and S‧‧‧π interactions in the crystal packing of 3-(phenylsulfinyl)-2H-chromen-2-one. An investigation of intermolecular interactions and crystal packing through Hirshfeld surface analysis reveals that the maximum of the close contacts are due to weak interactions.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1445 - 1455"},"PeriodicalIF":2.2,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145162197","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":"Mechanistic study of nitrone and maleimide [3 + 2] cycloaddition: a combined DFT, BET study, docking, and ADMET approach from the MEDT perspective","authors":"Raghad Mowafak Al-Mokhtar,&nbsp;Haydar Mohammad-Salim,&nbsp;Muheb Algso","doi":"10.1007/s11224-025-02455-0","DOIUrl":"10.1007/s11224-025-02455-0","url":null,"abstract":"<div><p>A [3 + 2] cycloaddition (32CA) reaction between maleimide (<b>MD1, MD2</b>) and nitrones (<b>NT1, NT2, NT3</b>) was investigated at the MPWB95/6-311G(d,p) level of theory utilizing Molecular Electron Density Theory (MEDT). Conceptual density functional theory (CDFT) indices substantiated the roles of maleimide (<b>MD1, MD2</b>) and nitrones (<b>NT1, NT2, NT3</b>) as electrophiles and nucleophiles, respectively. The reaction proceeds via two possible pathways: <b><i>exo</i></b> and <b><i>endo</i></b>. Investigation of the Potential Energy Surface (PES) revealed that the <b><i>exo</i></b> and <b><i>endo</i></b> pathways exhibit Gibbs free energy values of (− 13.84, − 13.82, − 12.31, − 14.18 kcal·mol^-1) and (− 8.78, − 7.87, − 7.88, − 8.54 kcal·mol^-1), respectively, indicating kinetically controlled, highly exothermic, and spontaneous reactions, as evidenced by negative ΔG values. The global electron density transfer (GEDT) values ranging from 0.08 to 0.19e suggest a low-polarity electron density transfer of the forward electron density flux (FEDF) type from nitrones (<b>NT1, NT2, NT3</b>) to maleimide (<b>MD1, MD2</b>), while local indices, particularly Parr functions, elucidate the electronic spin distribution. Analyses employing electron localization function (ELF) in conjunction with quantum theory of atoms in molecules (QTAIM) identified the nitrone species as participating in a one-step <i>zw-type</i> 32CA reaction. However, topological analysis of the electron density at the transition state demonstrated that these reactions proceed via a non-concerted mechanism. Bonding Evolution Theory (BET) analysis further elucidated the reaction mechanism, revealing six Structural Stability Domains (SSDs) and pseudoradical centers at the C4–C3 and C5–O1 bonds in the transition states. Molecular docking studies demonstrated that the cycloadducts (<b>IZ1, IZ2, IZ3</b>, and <b>IZ4</b>) exhibited binding energies (− 10.88, − 10.61, − 10.40, and − 11.68 kcal mol^-1) with the Michigan Cancer Foundation-7 (MCF-7) protein (3ERT) that were lower than the co-crystal ligand (− 13.10 kcal mol^-1). The in silico ADMET and drug-likeness predictions suggest promising potential for further investigation.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 5","pages":"1707 - 1727"},"PeriodicalIF":2.2,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145121396","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 investigation on [2π + 4π] cycloaddition mechanisms of buta-1,3-diene derivatives with sulfur dioxide: DFT and in silico study","authors":"Moulay Driss Mellaoui,&nbsp;Alejandro Morales-Bayuelo,&nbsp;Abdallah Imjjad,&nbsp;Haydar Mohammad-Salim,&nbsp;Zainab M. Almarhoon,&nbsp;Khalid Abbiche,&nbsp;Aaziz Jmiai,&nbsp;Souad El Issami,&nbsp;Hanane Zejli,&nbsp;Mohammad Shahidul Islam,&nbsp;Mahboob Alam","doi":"10.1007/s11224-025-02466-x","DOIUrl":"10.1007/s11224-025-02466-x","url":null,"abstract":"<div><p>The present study explores the [2π + 4π] cycloaddition reaction with the participation of a buta-1,3-diene series with sulfur dioxide. This investigation employs the molecular electron density theory (MEDT), using the 6-311G(d,p) basis set coupled with the MPWB1K method. Analysis of SO₂ reactivity reveals a predominance of the monosynaptic basin V(S2) with a population of 3.14 e and asymmetric NBO charges, where sulfur (1.597) acts as an electrophilic site. The study of chemical potentials shows that SO₂ (<i>μ</i> = 5.37 eV) reacts with dienes via polar interactions, primarily targeting the nucleophilic carbons C1 and C7. The activation energies, ranging from 10.44 to 14.95 kcal.mol⁻¹, indicate high barriers, with thermodynamically stable products (∆<i>G</i> range from − 7.35 to − 10.45 kcal.mol⁻¹). The ELF and QTAIM results reveal complex electronic reorganizations without covalent bonds at the transition states, highlighting significant non-covalent interactions. Among the products, P3 stands out for its high binding affinity (− 6.6 kcal.mol⁻¹) and promising ADMET profile, suggesting potential applications in molecular modeling and protein interaction, despite CYP1A2 inhibition.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1425 - 1443"},"PeriodicalIF":2.2,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145171355","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":"Nobel Prize for the discovery of microRNA and its role in gene regulation","authors":"Krisztina Hagymási","doi":"10.1007/s11224-025-02462-1","DOIUrl":"10.1007/s11224-025-02462-1","url":null,"abstract":"<div><p>The Nobel Prize 2024 in Physiology or Medicine has been awarded for the discovery of miRNA and its role in post-transcriptional gene regulation. Firstly, the results were thought to be irrelevant to humans, but nowadays, at least 30% of the known miRNAs could be used as novel biomarkers for screening human diseases and therapeutic purposes targeting manipulation of cell functions under examinations.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 2","pages":"759 - 765"},"PeriodicalIF":2.1,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143622176","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":"Superprismane carbon network as a sensing element for naphthylamine and toluidine molecules based on first-principles perspectives","authors":"M. S. Jyothi,&nbsp;V. Nagarajan,&nbsp;R. Chandiramouli","doi":"10.1007/s11224-025-02463-0","DOIUrl":"10.1007/s11224-025-02463-0","url":null,"abstract":"<div><p>Two of the major precursors used in the dye and chemical industries, 2-naphthylamine and o-toluidine were considered to adsorb on hydrogenated superprismane at three different orientations. Based on the formation energy of −6.245 eV/atom, the stable structure of hydrogenated superprismane was ensured; the material was further studied for its electronic properties and the electron distribution. The changes in bandgap energy, adsorption energies, charge transfer analysis, and percent adsorption energy gap were explored for hollow, parallel, and triangle orientation of 2-naphthylamine and o-toluidine on hydrogenated superprismane. The results indicate that the maximum reduction in band gap energy and increased interactions were observed for parallel site orientations. The presence of –NH₂, groups in both the target molecules and –CH₃ in o-toluidine, offered maximum interactions owing to π electrons of organic moieties and the dipole-dipole interactions. The results confer that the hydrogenated superprismane could efficiently adsorb 2-naphthylamine and o-toluidine molecules.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1397 - 1408"},"PeriodicalIF":2.2,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145171094","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":"Electronic structures and EDA-NOCV and absorption spectra analysis of Schiff base and pyridine derivatives mixed ligands in transition metal complexes","authors":"Ghouzala Boukehil,&nbsp;Mohamed Amine Zerizer,&nbsp;Sabri Mecheri,&nbsp;Bachir Zouchoune","doi":"10.1007/s11224-025-02465-y","DOIUrl":"10.1007/s11224-025-02465-y","url":null,"abstract":"<p>DFT calculations using BP86, PBE, and B3LYP functionals have been carried out on a series of complexes of the types [M(L1)(L2)]²⁺, [M(L2)₂]²⁺, [M(L2)(L3)₂]²⁺, and [M((L3)₄]²⁺ (M = Ni, Pd, Cu, Zn, and L1 = N-(4methoxybenzylidene) isonicotihydrazone bidentate Schiff base, L2 = 2,2′-bipyridine, and L3 = pyridine). A complete rationalization of bonding is provided of these kinds of complexes, where the predicted structures provide to the M(II) cations a perfect square planar geometry for Ni(II), Pd(II), and Cu(II) and a tetrahedral one for Zn(II). Large HOMO–LUMO gaps are calculated for all optimized structures of singlet spin state except for Cu(II) with a doublet spin state; suggesting a good kinetic stability. The low singlet spin state for Ni(II), Pd(II), and Zn(II) and the doublet spin state for Cu(II) complexes are characterized by BP86, PBE, and B3LYP functionals as ground states compared to those of high triplet and quartet spin ones, respectively. The TD-DFT theoretical study performed on the optimized geometries permitted us to predict the UV–Vis spectra and to pinpoint accurately the spectral positions and the nature of the different electronic transitions according to their molecular orbital localization; hence, the available experimental UV–Vis spectra are compared to our findings. The electronic spectra obtained in ethanol solvent show red shifts for complexed species due to the coordination of free ligands with metal cations characterized by HOMO → LUMO and HOMO-1 → LUMO electronic transitions.</p>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1381 - 1395"},"PeriodicalIF":2.2,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145170819","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":"Baruch S. Blumberg’s centennial—a Nobel laureate cutting through scientific disciplines","authors":"Istvan Hargittai","doi":"10.1007/s11224-025-02461-2","DOIUrl":"10.1007/s11224-025-02461-2","url":null,"abstract":"<div><p>Baruch S. Blumberg (1925˗2011), MD, PhD, started out in physics then moved to chemistry, finally, became a physician and research scientist. At an early stage, he worked with polysaccharides and returned to them at a later stage of his career. He received the Nobel Prize for the discovery of the Hepatitis B virus and the invention of the vaccine to protect against it. He concluded his career as director of the NASA Astrobiology Institute.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1527 - 1530"},"PeriodicalIF":2.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145169321","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":"Strategies with spectroscopic and optical insights for optoelectronic applications of novel synthesized Schiff base: impact of nitro group","authors":"Anjali Jha,&nbsp;B. Rajesh Kumar,&nbsp;RaviShankar Kumar Ch","doi":"10.1007/s11224-025-02457-y","DOIUrl":"10.1007/s11224-025-02457-y","url":null,"abstract":"<div><p>Optical materials organic in nature are leading materials exhibiting semiconducting properties which is a trend of present technology for optical and electronic applications. Active organic materials of Schiff bases are of vital importance in terms of their molecular properties, band gap, refractive index, and dielectric operated at room temperature compared to inorganic materials at elevated temperatures during synthesis. The article focuses on the development of thin films with green synthesis of Schiff base of 4-hydroxy benzaldehydes with different anilines for optoelectronic applications. The formation of the Schiff base compounds was confirmed with spectroscopic methods showing shifts in wavenumbers in infrared spectra, transition with optical band gap in ultraviolet spectra, and chemical environment with chemical shifts using proton NMR. Powdered XRD provided information of structure, composition, and crystalline proximity of the synthesized Schiff base compounds. Optical properties such as refractive index and dielectric constant were attributed with spectroscopic ellipsometer. Computational studies were performed using the Gaussian 16 package with the B3LYP method basis set 6–311 +  + ** for all molecular compounds to confirm the molecular structures, optimized geometry, and electronic and optical properties. The insights of these properties are best visualized in terms of quantum mechanical descriptors responsible for changes in electron density. Studies of synthesized Schiff base compounds with nitro groups find widespread use in variety of applications and can be employed as excellent organic semiconducting material with an energy gap of 3.08 eV, refractive index of 2.074, and dielectric constant of 4.303.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1355 - 1368"},"PeriodicalIF":2.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145168070","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":"DFT study of Pt-rGO as a potential catalyst for glycerol hydrodeoxygenation into propanediols","authors":"Patrik Chandra,&nbsp;T. Triyono,&nbsp;Wega Trisunaryanti,&nbsp;Lala Adetia Marlina,&nbsp;Aulia Sukma Hutama","doi":"10.1007/s11224-025-02454-1","DOIUrl":"10.1007/s11224-025-02454-1","url":null,"abstract":"<div><p>Catalytic glycerol hydrodeoxygenation is one of the attractive chemical reactions that can overcome the issue of glycerol overproduction. The performances of platinum-based catalysts have been widely investigated, but little is known about the role of platinum in the hydrodeoxygenation process. This research studied platinum-reduced graphene oxide’s structure and electronic properties using the DFT method and PBEsol functional. Adsorption of glycerol, 1,2-propanediol, and 1,3-propanediol on the Pt-rGO system were all chemisorption proven by the interaction energy value of − 4.34, − 3.78, and − 3.15 eV, respectively. Charge density analysis reveals an enhanced electron transfer process between Pt and rGO compared to the Pt-graphene system. Based on the activation energy, the production of 1,2-propanediol is more favorable when Pt-rGO is used as the catalyst. The rate-determining step was the C-H bond formation with an activation energy of 0.75 eV. This study provides additional insight into the role and performance of platinum-based catalysts in glycerol hydrodeoxygenation reactions.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"36 4","pages":"1369 - 1379"},"PeriodicalIF":2.2,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145169323","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}