Structural Chemistry最新文献

{"title":"Computational design of graphene oxide-based delivery of PD128763 PARP inhibitor: DFT, molecular dynamics, and molecular docking analysis","authors":"Fahime Alikhoshi,&nbsp;Mehdi Sadeghi,&nbsp;Ali Arab","doi":"10.1007/s11224-025-02692-3","DOIUrl":"10.1007/s11224-025-02692-3","url":null,"abstract":"<div><p>In this study, the anticancer drug PD128763 was evaluated for its interaction with graphene oxide as a nanocarrier and with the Poly(ADP-ribose) Polymerase (PARP) protein (PDB ID: 5HA9), using computational approaches. Density functional theory (DFT) calculations revealed favorable adsorption energies, indicating the thermodynamic stability of the drug-carrier complex. Quantum theory of atoms in molecules (QTAIM) analyses confirmed noncovalent interactions along with significant hydrogen bonds. UV-Vis spectra exhibited shifts due to charge transfer and electronic polarization effects. Solvent studies showed enhanced stability in polar media. Molecular docking of PD128763 with PARP revealed strong binding affinity and interactions with key active site residues. Subsequently, a 130 ns molecular dynamics (MD) simulation of the drug-protein complex was performed. The results confirmed the structural stability and strong interactions within the binding site. These findings suggest that PD128763 exhibits stable and effective binding both on the graphene oxide surface and with its biological target, proposing it as a suitable candidate for targeted anticancer drug delivery.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2621 - 2636"},"PeriodicalIF":2.3,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950492","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":"Magnetic bistability of stilbene radical derivatives: a DFT and CASSCF study","authors":"Andrey G. Starikov,&nbsp;Maxim G. Chegerev,&nbsp;Alyona A. Starikova,&nbsp;Vladimir I. Minkin","doi":"10.1007/s11224-025-02687-0","DOIUrl":"10.1007/s11224-025-02687-0","url":null,"abstract":"<div><p>The field of organic molecular magnets is rapidly advancing, and the current efforts of the researchers are aimed at uncovering their full potential for applications in quantum computing, molecular electronics and other emerging technologies. The goal of this work was to search for new structural motifs of organic compounds undergoing spin-state-switching rearrangements. With this in mind, stilbene derivatives comprising two fluorenyl or <i>tert</i>-butyl nitroxide radicals were investigated by means of quantum chemical modeling of their electronic structures, isomerization and magnetic properties. The results obtained using various DFT functionals (B3LYP-D3BJ, M05-2X and wB97XD) were proved by multi-configurational CASSCF/NEVPT2 calculations. The possibility of photoinduced transitions between the paramagnetic <i>cis</i> isomers (<i>S</i> = 1) and diamagnetic <i>cyclic</i> forms (<i>S</i> = 0) has been revealed, allowing us to consider the studied compounds as potential organic magnetic switches.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2637 - 2649"},"PeriodicalIF":2.3,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950493","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":"Effect of hydrogen bond donating groups in N,N(^{prime })-substituted naphthalenediimides on fluoride ion binding and redox behavior","authors":"Oscar Uriel Villanueva-Contreras,&nbsp;José A. Alatorre-Barajas,&nbsp;Adrián Ochoa-Terán,&nbsp;Jesús Jara-Cortés,&nbsp;Mariana Martínez-Galván,&nbsp;Georgina Pina-Luis","doi":"10.1007/s11224-025-02667-4","DOIUrl":"10.1007/s11224-025-02667-4","url":null,"abstract":"<div><p>In this work, we investigate the influence of hydrogen donor groups and spacer chain length in N,N<span>(^{prime })</span>-substituted naphthalenediimides (NDIs) on fluoride binding affinity and redox behavior through combined experimental and theoretical approaches. UV-vis spectroscopy reveals that while benzylic substituents connected via methylene spacers minimally affect optical properties, they significantly modulate <span>(pi)</span>-acidity and reduction potentials. Systematic titrations with <span>(text {F}^-)</span> and the analysis of the absorbance profiles demonstrate that hydrogen donor groups enhance fluoride binding capacity, leading to multi-anion complexes with stoichiometries of 3-5 fluoride ions per NDI. However, binding affinity does not correlate directly with radical formation efficiency. Electronic structure calculations confirm the formation of stable NDI-fluoride complexes and reveal that direct electron transfer from <span>(text {F}^-)</span> to NDIs is thermodynamically unfavorable (<span>(varvec{Delta G=3.19-3.28})</span> eV). Solvent-mediated pathways involving <span>(text {DMSO}^{bullet -})</span> approach thermodynamic feasibility but face significant kinetic barriers (<span>(varvec{Delta G^{dagger }=1.03})</span> eV). To reconcile these contradictions with experimental observations, we explore a photophysical mechanism based on low-lying <span>(varvec{text {p}rightarrow pi ^{*}})</span>excited states in NDI-DMSO-fluoride complexes, which suggests that photoexcitation could drive barrierless electron transfer pathways with DMSO acting as a scavenger for reactive <span>(text {F}^{bullet })</span> radicals. This work demonstrates the complex interplay between structural features, anion binding, and redox chemistry in NDI systems, while identifying key mechanistic uncertainties that warrant further investigation through experimental an theoretical studies. The findings have implications for rational design of NDI-based fluoride sensors and highlight the potential role of photochemical processes in anion-induced electron transfer reactions.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2607 - 2620"},"PeriodicalIF":2.3,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950512","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":"Unusual cation···cation interactions in pure and mixed Zundel salts of 4H-[1,2,3]triazolo[4,5-c][1,2,5]oxadiazole 5-oxide","authors":"Ivan V. Fedyanin,&nbsp;Alexey A. Voronin","doi":"10.1007/s11224-025-02691-4","DOIUrl":"10.1007/s11224-025-02691-4","url":null,"abstract":"<div><p>Three new salts of 4H-[1,2,3]triazolo[4,5-c][1,2,5]oxadiazole 5-oxide containing the Zundel (H₅O₂⁺) cation were obtained, including a binary salt and two mixed isostructural salts with potassium and ammonium cations. Their structures were determined using single-crystal X-ray diffraction and analyzed by periodic PBE0-D3/POB-TZVP calculations, employing geometrical descriptors and topological analysis of the electron density. The anion shows consistent characteristics across all three salts, retaining approximate C_2v symmetry in geometry, bond critical point properties, and atomic charges. Formation of the anion increases the aromaticity of the triazole ring and contributes to the acidity of the H-form and the stability of the deprotonated form. In contrast, the Zundel cations exhibit different geometries, being closer to <i>cis</i> in the binary salt and <i>trans</i> in the mixed salts, although the O···O distance remains comparable, as do the atomic charges and the topological description of the bonding interactions. DFT calculations reveal that the cation is asymmetric in all cases, and that the degree of asymmetry depends on the nature of the second cation in the mixed salts. Atomic-charge analysis indicates that the positive charge in the Zundel cation is concentrated on the central hydrogen atom, enabling unusual bonding cation···cation interactions formed by the terminal atoms, as evidenced by the presence of bond critical points between the atoms of the cations. Thus, besides typical cation···anion and π-stacking anion···anion contacts, the salts feature direct cation···cation interactions. In the mixed salts these interactions lead to the formation of cationic chains with relatively strong bonds, whereas in the binary salt cationic chains of a different geometry are also present but exhibit much lower, van der Waals-type interaction energies. </p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 3","pages":"1165 - 1176"},"PeriodicalIF":2.2,"publicationDate":"2025-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147938072","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":"Structure-optical, linear and nonlinear optical properties relationship in thiazolidine-amides","authors":"Mostefa Boumediene,&nbsp;Benamar Baroudi,&nbsp;Toufik Bensafi,&nbsp;Djebar Hadji","doi":"10.1007/s11224-025-02671-8","DOIUrl":"10.1007/s11224-025-02671-8","url":null,"abstract":"<div><p>Five thiazolidine amides, including several substituents, were studied for their possible activity in nonlinear optical applications using quantum chemical calculations at multiple levels. Several properties, including linear and nonlinear optical properties, HOMO and LUMO energies, energy gap, and reactivity parameters, have been calculated and analyzed. High first hyperpolarizability <i>β</i>_tot up to 1217.15 and 1546.58 a.u. was obtained for the thiazolidines with chlorine <b>THA@Cl</b> and two fluorines <b>THA@FF</b>, respectively, suggesting strong nonlinear optical activity. A direct correlation was achieved between the <i>β</i>_tot and the energy gap <i>E</i>_g and between the <i>β</i>_HRS and <i>β</i>_//. The study indicates that the frontier molecular surfaces play an important role in the high qualitative interpretation of the chemical reactivity of these thiazolidines. Frontier molecular orbitals show that the HOMO density is located over thiazolidine and phenyl rings, and the LUMO isodensity is shifted towards the phenyl attached with electron acceptor groups. <b>THA@Cl</b> and <b>THA@FF</b> could be suggested as potential high-performance optoelectronic materials.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2587 - 2605"},"PeriodicalIF":2.3,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950491","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":"James D. Watson (1928–2025)","authors":"Istvan Hargittai","doi":"10.1007/s11224-025-02682-5","DOIUrl":"10.1007/s11224-025-02682-5","url":null,"abstract":"<div><p>James D. Watson, arguably the most famous scientist of the second half of the 20th century, passed away on November 6, 2025. He was the co-discoverer (with Francis Crick) of the double helix structure of DNA, which is widely considered the greatest biological discovery of the 20th century. He wrote the epoch-making book on the discovery’s story, pioneered methods in textbook writing, initiated and managed the US Human Genome Project; and developed Cold Spring Harbor Laboratory into a leading international biomedical research center. In the last phase of his life, he lost the respect of the research community due to his racist statements.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 1","pages":"1 - 3"},"PeriodicalIF":2.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146043450","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":"Structural diversity and the role of solvents in supramolecular arrangement of FeIIIPc(CN)(H2O) solvate crystals","authors":"Anton Fedonin, Kirill Metlushka, Ruzal Zinnatullin, Kamil Ivshin, Airat Kiiamov, Dmitry V. Zakharychev, Ayrat R. Khamatgalimov, Marco Naumann, M. Knupfer, Olga Kataeva","doi":"10.1007/s11224-025-02686-1","DOIUrl":"https://doi.org/10.1007/s11224-025-02686-1","url":null,"abstract":"","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147332660","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":"Challenging the established view of Lewis-type interactions as formulated within quantum chemical topology: an interpretation of Si–Pt and M–Pt (M = Ga, In, and Sn) bonding in terms of electronic force fields","authors":"Sergey V. Kartashov,&nbsp;Anton P. Fedonin,&nbsp;Julia R. Khusnutdinova,&nbsp;Robert R. Fayzullin","doi":"10.1007/s11224-025-02604-5","DOIUrl":"10.1007/s11224-025-02604-5","url":null,"abstract":"<div><p>This work investigates the nature of the Si–Pt, M–Pt (M = Ga, In, and Sn), and other coordinate bonds within a family of cationic complexes, analyzed through the superposition of the electrostatic force field <span>(mathbf{F}_{text{es}}(mathbf{r}))</span>, the total static force field <span>(mathcal{F}(mathbf{r}))</span>, and the electron density gradient <span>(nablarho(mathbf{r}))</span>. It has been demonstrated that the Si–Pt coordinate bond represents a polar interatomic interaction exhibiting a pronounced covalent contribution to the transferred electronic charge and a notable localization of the Fermi exchange hole density <span>(h_{x}(mathbf{r}, mathbf{r}'))</span>. Within this interaction, the zero-flux surface in <span>(nablarho(mathbf{r}))</span> is located closer to the Si nucleus of the Lewis-basic atom that provides its electron pair to the internuclear binding region, whereas the zero-flux surface in <span>(mathbf{F}_{text{es}}(mathbf{r}))</span> lies closer to the Pt nucleus of the Lewis-acidic atom that hosts the subatomic electrophilic site. Consequently, the Si–Pt bond fails both to meet the criterion for the categorization of Lewis-type interactions and to conform to the underlying concept of electrophilic influence zones—these two constructs being theoretically arbitrary, yet methodologically well-established within quantum chemical topology. Instead, an interpretation predicated upon interatomic charge transfer and articulated within the framework of force-field pseudoatoms in molecules has been advanced as a compelling alternative. The Lewis-type character of the Si–Pt bond has been elucidated through the analysis of the exchange charge density <span>(q_x(mathbf{r})= nabla cdot mathbf{F}_{x}(mathbf{r})/(4pi))</span>, the fermionic force <span>(mathbf{F}_{text{f}}(mathbf{r}))</span>, and the component contribution of the exchange force <span>(mathbf{F}_{x}(mathbf{r}))</span> to <span>(mathcal{F}(mathbf{r}))</span>, expressed as <span>(left[mathbf{F}_{x}(mathbf{r})cdot mathcal{F}(mathbf{r})right]/|mathcal{F}(mathbf{r})|)</span>.</p><h3>Graphical Abstract</h3>\u0000<div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 4","pages":"1901 - 1917"},"PeriodicalIF":2.3,"publicationDate":"2025-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148614344","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":"Tuning D- π-A dyes for efficient performance: a two-step strategy via π-bridge and electron donor optimization","authors":"Kun Wang,&nbsp;Zheng Wei,&nbsp;Yan Cui,&nbsp;Yao Liang,&nbsp;Hualong Tao,&nbsp;Ming He,&nbsp;Teng-Fei Lu,&nbsp;Zhihua Zhang","doi":"10.1007/s11224-025-02680-7","DOIUrl":"10.1007/s11224-025-02680-7","url":null,"abstract":"<div><p>This study investigates the effects of promising electron donors and modified π-bridge structures in organic dyes on the photoelectronic properties and charge transfer dynamics of solar cells. Using density functional theory (DFT) and time-dependent DFT (TD-DFT), the geometric, electronic structures and optical properties were systematically investigated via a two-step design strategy: initial optimization by π-bridge modification, followed by further refinement through precise electron-donor regulation. Additionally, quantum dynamics simulations were employed to clarify how these two strategies influence charge transfer at the dye/TiO₂ interface. The calculation results indicate that, compared with <b>B1</b> dye, the addition of a planar-conjugated thiophene to modify the π-bridge effectively broadens the spectral absorption range and enhances the donor-acceptor coupling and charge injection at the dye/TiO₂ interface. The non-planar propeller-shaped 4,4’-dimethoxytriphenylamine groups (<b>D1</b>), endowed with excellent electron-donating properties, exhibit superior light-harvesting capability and synergistically enhance the electron transport performance of the dye through conjugation effects with the thiophene π-bridge. Overall, these findings significantly deepen our understanding of the effects of structural modifications in organic dyes and provide valuable insights for designing efficient dye sensitizers.</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2541 - 2555"},"PeriodicalIF":2.3,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950517","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/TD-DFT studies on carbazole-diphenylamine-based dyes using different π-bridges for DSSCs","authors":"Tomás Delgado-Montiel,&nbsp;Rody Soto-Rojo,&nbsp;Samuel Soto-Acosta,&nbsp;Carlos A. Peñuelas,&nbsp;María Edith Ruelas-Ávila,&nbsp;Alberto Baez-Castro,&nbsp;Manuel Luque-Román,&nbsp;Daniel Glossman-Mitnik,&nbsp;Jesús Baldenebro-López","doi":"10.1007/s11224-025-02597-1","DOIUrl":"10.1007/s11224-025-02597-1","url":null,"abstract":"<div><p>Molecular engineering of metal-free organic sensitizers with a Donor-π-Acceptor (D-π-A) structure is fundamental for the development of next-generation dye-sensitized solar cells (DSSCs). In this work, we present a systematic study based on Density Functional Theory (DFT) and its Time-Dependent extension (TD-DFT) on a series of eight novel dyes integrating a potent hybrid carbazole-diphenylamine donor unit and a cyanoacrylic acid anchor. The research elucidates how the chemical constitution of various conjugated (π) bridges modulates a comprehensive set of structural, electronic, optical, and charge-transport properties. Our findings reveal that molecular planarity, quantitatively assessed using dihedral angles and planarity parameters (MPP/SDP), is a critical performance factor. Specifically, the incorporation of thiophene-based π-bridge promotes superior planarity, leading to a significant reduction in chemical hardness and promoting efficient intramolecular charge transfer (ICT), a conclusion visually corroborated by Transition Density Matrix (TDM) analysis. Furthermore, the calculation of reorganization energies indicates that the designed dyes possess favorable intrinsic kinetics for ambipolar charge transport. Among the evaluated candidates, the sensitizer DC5A, incorporating a benzodithiophene bridge, is identified as exceptionally promising, exhibiting a red-shifted absorption maximum of 645 nm, a HOMO–LUMO energy gap of 2.60 eV, and free energy of electron injection of 0.80 eV. This study not only identifies a series of synthesis-feasible dyes with high potential for photovoltaic applications but also establishes a key design principle, the use of planar bridges to enhance ICT in D-π-A systems, offering a clear and rational route for the development of future high-efficiency organic photosensitizers.\u0000</p></div>","PeriodicalId":780,"journal":{"name":"Structural Chemistry","volume":"37 5","pages":"2567 - 2586"},"PeriodicalIF":2.3,"publicationDate":"2025-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148950490","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}