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Search Results (192)

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Keywords = DFT reactivity indices

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28 pages, 16105 KB  
Article
Physicochemical Assessment of Selected Conductive Polymers for Probable Mercury Remediation in Wastewater—Experimental and DFT Approach
by Sesona Macanda, Hassan Shoyiga, Adeniyi Ogunlaja, Uliana Pinaeva, Sizwe Zamisa and Nobathembu Faleni
Analytica 2026, 7(3), 55; https://doi.org/10.3390/analytica7030055 - 13 Aug 2026
Viewed by 65
Abstract
Mercury contamination in aquatic environments poses significant risks to ecosystems and human health, underscoring the need for effective remediation technologies. This research examines the physicochemical properties of the synthesised polymer materials, and DFT calculations were used as an initial step for material development [...] Read more.
Mercury contamination in aquatic environments poses significant risks to ecosystems and human health, underscoring the need for effective remediation technologies. This research examines the physicochemical properties of the synthesised polymer materials, and DFT calculations were used as an initial step for material development to validate our experimental outcomes for the prepared polymers: polyaniline (PANI), polyethersulfone (PES), and polyamidoamine (PAMAM). Furthermore, DFT studies were used to elucidate structure–property relationships in polymers, serving as performance predictors for mercury adsorption and selectivity, as well as for their applicability in electronic sensors. The characterisation techniques indicated the high functional group densities of PAMAM dendrimers for effective chelation, while the semi-crystalline structure of PANI improves metal binding. DFT calculations reveal that PAMAM exhibits the smallest HOMO–LUMO energy gap, indicating a high reactivity towards mercury ions. Binding energies indicate that PAMAM forms the most stable single-ion complex; PAM1Hg (0.242 eV, 23.37 kJ mol−1), whereas PES exhibits enhanced interaction at elevated mercury concentrations, resulting in stable multi-Hg complexes, PES3Hg (0.136 eV, 13.13 kJ/mol). The findings indicate that nitrogen-rich functional groups and aromatic systems play a crucial role in mercury binding, highlighting the promise of conductive polymers for creating effective adsorbents aimed at mercury remediation in industrial wastewater. Full article
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16 pages, 15102 KB  
Article
Positional Isomers of B6C6N6 Nanorings: Stability, Reactivity, and Optical Properties from First Principles
by Xin Chen, Peipei Li and Shusheng Gong
Nanomaterials 2026, 16(15), 953; https://doi.org/10.3390/nano16150953 - 3 Aug 2026
Viewed by 254
Abstract
The positional arrangement of BN and CC units in B6C6N6 cyclic nanorings profoundly influences their stability, electronic structure, optical response, and reactivity. Here, we comparatively investigate eight positional isomers (C1–C8) using DFT and TD-DFT calculations. Among C1–C8, C1 [...] Read more.
The positional arrangement of BN and CC units in B6C6N6 cyclic nanorings profoundly influences their stability, electronic structure, optical response, and reactivity. Here, we comparatively investigate eight positional isomers (C1–C8) using DFT and TD-DFT calculations. Among C1–C8, C1 is the most stable, and C8 is the most unstable in the range of 200–1000 K. Their relative stability is governed by B-N charge separation, homonuclear B-B and N-N defects (charge repulsion), and bond-angle distortion (ring tension). The HOMO–LUMO gaps range from 4.40 eV (C3) to 8.45 eV (C2), indicating distinct kinetic stability. Aromaticity analysis reveals that all isomers are nonaromatic. In the gas phase, the lowest-energy absorption bands of C1 and C3 are located at about 429 nm and 606 nm, respectively. Due to different transition mechanisms, namely locally excited (LE) for the former and charge-transfer (CT) for the latter, solvent polarity has dramatically different influence on these two absorption bands. Compared to their positions in the gas phase, these absorption bands are blue-shifted about 20 nm and 220 nm in water, respectively. Reactivity analysis identifies the B-B bond in C7 as the strongest electrophilic site (LEAE = −2.93 eV), with the surrounding framework serving as nucleophilic domains, endowing C7 with the strongest bifunctional reactivity. This work establishes a comprehensive structure–property map for B6C6N6 isomers, providing guidance for designing BCN-based nanorings for catalysis, molecular recognition, and optoelectronics. Full article
(This article belongs to the Section Theory and Simulation of Nanostructures)
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21 pages, 2462 KB  
Article
Experimental and Theoretical Insights on the Use of Expired Furosemide as Corrosion Inhibition for Cu in NaCl
by Dalia Garcia-Rosas, Alfredo Brito-Franco, Hugo Albeiro Saldarriaga-Noreña, Roy Lopez-Sesenes, America Maria Ramirez-Arteaga, Ana Karen Galvez-Larios, Jesus Porcayo-Calderon and Jose Gonzalo Gonzalez-Rodriguez
Materials 2026, 19(15), 3274; https://doi.org/10.3390/ma19153274 - 3 Aug 2026
Viewed by 211
Abstract
Copper and its alloys are extensively employed in a broad range of industrial applications owing to their outstanding mechanical, electrical, and thermal properties. However, their susceptibility to corrosion in aggressive environments remains a major challenge, making corrosion inhibitors one of the most practical [...] Read more.
Copper and its alloys are extensively employed in a broad range of industrial applications owing to their outstanding mechanical, electrical, and thermal properties. However, their susceptibility to corrosion in aggressive environments remains a major challenge, making corrosion inhibitors one of the most practical and cost-effective strategies for extending their service life. Nevertheless, conventional synthetic inhibitors are often limited by their high cost and adverse environmental and health impacts resulting from their toxicity. In this context, the present work provides a comprehensive experimental and theoretical assessment of the corrosion inhibition performance of Furosemide as an environmentally friendly inhibitor for copper in 3.5 wt.% NaCl solution. The corrosion inhibition performance was evaluated experimentally through gravimetric measurements, potentiodynamic polarization, and electrochemical impedance spectroscopy (EIS), while the adsorption behavior of Furosemide was investigated using density functional theory (DFT) calculations. The results demonstrated that expired Furosemide effectively reduced the corrosion rate of copper, with the inhibition efficiency increasing as the inhibitor concentration increased and decreased with increasing temperature. A maximum inhibition efficiency of 90% was achieved at an inhibitor concentration of 400 ppm. The calculated Gibbs free energy of adsorption indicated that Furosemide adsorbs onto the copper surface through a mixed physisorption–chemisorption mechanism, following the Langmuir adsorption isotherm. Potentiodynamic polarization measurements further revealed that Furosemide predominantly suppresses the anodic dissolution reaction, indicating that it behaves as an anodic-type corrosion inhibitor. In addition, the presence of Furosemide significantly decreased the passive current density and shifted the breakdown potential toward more positive values, demonstrating an enhancement in the stability and protective character of the passive film. Electrochemical impedance spectroscopy showed that the corrosion process was governed by diffusion-controlled kinetics in the uninhibited solution, whereas the addition of Furosemide changed the corrosion mechanism to a charge-transfer-controlled process. Density functional theory (DFT) calculations provided additional insight into the inhibition mechanism of Furosemide. The calculated EHOMO) and ELUMO values indicate that the molecule can both donate and accept electrons, reflecting its nucleophilic and electrophilic character and its strong affinity for adsorption on the copper surface. Furthermore, the relatively small energy gap (4.631 eV) suggests high molecular reactivity and facilitates electronic interactions with the metal surface. The estimated fraction of electrons transferred further supports the electron-donating ability of Furosemide during the adsorption process. Differences between the Fukui functions and the molecular electrostatic potential (MEP) maps are attributed to the distinct chemical information provided by each descriptor. Whereas the Fukui functions identify the most reactive atomic sites involved in soft donor–acceptor interactions, the MEP maps describe the molecular charge distribution governing electrostatic (hard–hard) interactions. Full article
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32 pages, 26755 KB  
Article
Novel Sulfonate Derivatives Functionalized with Triazole–Hydrazone Moieties: Synthesis, Characterization, DFT, Targeting Brain Tumors via DNA Damage, Cytotoxicity, Migration Suppression, Antimicrobial Activity, and In Silico Study
by Yasemin Ünver, Meryem Evecen, Fatih Çelik, Ali Aydın, Halil İbrahim Güler, Kadriye İnan Bektaş and Tuğba Usta
Molecules 2026, 31(13), 2281; https://doi.org/10.3390/molecules31132281 - 30 Jun 2026
Viewed by 517
Abstract
In this study, a new series of (E)-4-((2-(2-(4-amino-3-methyl-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl)acetyl)hydrazono)methyl)phenyl 4-halogenobenzenesulfonates (3a3d), where 3a = F, 3b = Cl, 3c = Br, and 3d = I, were successfully synthesized via a straightforward synthetic route. The structures of the obtained compounds were [...] Read more.
In this study, a new series of (E)-4-((2-(2-(4-amino-3-methyl-5-oxo-4,5-dihydro-1H-1,2,4-triazol-1-yl)acetyl)hydrazono)methyl)phenyl 4-halogenobenzenesulfonates (3a3d), where 3a = F, 3b = Cl, 3c = Br, and 3d = I, were successfully synthesized via a straightforward synthetic route. The structures of the obtained compounds were fully characterized and confirmed by spectroscopic techniques, including FT-IR, 1H NMR, and 13C NMR, as well as LC-MS/MS analysis. 1,2,4-triazole-based hydrazone derivatives (3a3d) were investigated using IR and NMR spectroscopy and DFT calculations. Intermolecular interactions, HOMO-LUMO, dipole moment, polarization, first-order hyperpolarizability, and molecular electrostatic potential studies on the molecules were examined. The HOMO and LUMO energy gap study supports the charge transfer probability in the molecules. These were conducted to investigate the reactivity and stability of heterocyclic molecules in bioactivity analysis. Electron density mapping within the molecular electrostatic potential plot and electrostatic potential representation within the iso-surface plot evaluated the concept of charge distribution in the molecule as nucleophilic reactions and electrophilic regions. The predicted nonlinear optical (NLO) properties of the molecules are much greater than those of urea. The results obtained from these investigations collectively provide evidence that the molecules possess nonlinear optical applications. Novel triazole–hydrazone-functionalized aryl sulfonate derivatives (3a3d) were evaluated for their anticancer potential against a panel of brain and non-brain cancer cell lines. Compound 3b exhibited the most favorable overall biological profile, displaying potent activity against SH-SY5Y neuroblastoma (GI = 7.59 μM) and U87MG glioblastoma cells (GI = 13.85 μM), together with the lowest toxicity toward normal FL fibroblasts (GI = 62.02 μM). Compounds 3c and 3d demonstrated remarkable potency against IDHmut-U87 glioma cells (GI = 3.87 and 3.27 μM, respectively), although their selectivity toward cancer cells was limited. DNA degradation studies revealed substantial fragmentation, particularly in C6 and SH-SY5Y cells, while migration assays indicated reduced cellular motility. Molecular docking studies identified compound 3b as the strongest PI3Kα binder, supporting a possible. In addition, the antimicrobial activities of compounds 3a3d were evaluated against selected Gram-positive and Gram-negative bacteria as well as Candida species using the broth microdilution method. The compounds exhibited measurable antimicrobial effects with MIC values ranging from 156 to 625 µg/mL, showing moderate growth inhibition against the tested microorganisms. Although the observed activity was lower than that of the reference antimicrobial agents, the results indicate that these triazole–hydrazone derivatives possess a detectable level of antimicrobial activity and provide a basis for further structural optimization. Collectively, the results suggest that compound 3b represents the most promising lead structure due to its balanced combination of potency, selectivity, and predicted target engagement. Molecular docking was performed to evaluate the binding potential of newly synthesized triazole derivatives (3a3d) against PI3Kα. The docking protocol was validated by re-docking alpelisib, yielding an RMSD of 0.64 Å. Among the tested compounds, 3b showed the most favorable binding energy (−9.94 kcal/mol) and estimated Ki value (52.13 nM), consistent with its superior in vitro activity. Its interactions with key PI3Kα residues, including Val851, Ser854, Met922, and Asp933, support a stable binding mode within the ATP-binding pocket. In silico ADME and toxicity analyses suggested acceptable drug-likeness characteristics, absence of major hepatotoxic, mutagenic, and carcinogenic liabilities, and moderate predicted acute toxicity profiles. These findings suggest that 3b is the most promising derivative for further validation. Full article
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26 pages, 4745 KB  
Article
Therapeutic Innovation from Plant-Derived Thai Herbal Extracts: α-Glucosidase Inhibitory Activity, Mechanistic Insights and Formulation Potential of the Selected Thai Rejuvenation Remedy
by Suthinee Sangkanu, Thanet Pitakbut, Chotika Buekhuntod, Sathianpong Phoopha, Jiraporn Khanansuk, Wandee Udomuksorn, Kasemsiri Chandarajoti and Sukanya Dej-adisai
Life 2026, 16(7), 1084; https://doi.org/10.3390/life16071084 - 28 Jun 2026
Viewed by 667
Abstract
This study highlights the therapeutic innovation potential of bioactive plant extracts derived from the selected Thai Rejuvenation Remedy 2 (TRJ 2) for antidiabetic applications. By integrating phytochemical profiling with in vitro α-glucosidase inhibition assays and in silico analyses, including molecular docking and density [...] Read more.
This study highlights the therapeutic innovation potential of bioactive plant extracts derived from the selected Thai Rejuvenation Remedy 2 (TRJ 2) for antidiabetic applications. By integrating phytochemical profiling with in vitro α-glucosidase inhibition assays and in silico analyses, including molecular docking and density functional theory (DFT), a comprehensive evaluation of the extract’s bioactivity and mechanistic basis was achieved. The findings demonstrate that both the relative abundance and chemical reactivity of constituent compounds contribute to the overall inhibitory effect through synergistic and competitive interactions. Piperine was identified as a potential bioactive metabolite, with a theoretically strong binding affinity and high reactivity toward the target enzyme. Among the tested extracts, the 80% ethanol extract exhibited the highest inhibitory activity (IC50 = 34.32 µg/mL), underscoring the importance of extraction optimization for maximizing therapeutic efficacy. Furthermore, formulation of the extract with cyclodextrin significantly enhanced solubility and improved pharmaceutical characteristics, meeting the quality requirements of the Thai Herbal Pharmacopoeia (THP). However, the detection of cadmium slightly above permissible levels indicates the need for stricter raw material quality control. Overall, TRJ 2 represents a promising source of bioactive plant-derived compounds and a viable candidate for development into innovative, ready-to-use herbal therapeutics for diabetes management. Full article
(This article belongs to the Special Issue Therapeutic Innovations from Plants and Their Bioactive Extracts)
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21 pages, 12870 KB  
Article
Mechanistic Insights into Comonomer Effects on Propylene Polymerization over TiCl3 Catalysts
by Lu Wang, Chao Yu, Yiwa Wang, Xiuming Liu, Jingnan Li, Lili Ma, Jiamei Wei, Zerun Zhao, Wanru Feng, Zhanggui Hou and Songbao Fu
Catalysts 2026, 16(7), 576; https://doi.org/10.3390/catal16070576 - 23 Jun 2026
Viewed by 356
Abstract
Incorporating comonomers in propylene polymerization plays a critical role in tuning the physical and chemical properties of the resulting polymers. In this study, the impact of three developed comonomers on propylene polymerization over the triethylaluminum-treated TiCl3 catalyst was investigated in detail by [...] Read more.
Incorporating comonomers in propylene polymerization plays a critical role in tuning the physical and chemical properties of the resulting polymers. In this study, the impact of three developed comonomers on propylene polymerization over the triethylaluminum-treated TiCl3 catalyst was investigated in detail by DFT. The results indicate that these comonomers remain highly stable under actual catalytic conditions, with their ions or functional groups showing a low propensity for detachment, which would otherwise poison the catalyst or disrupt the polymerization process. However, the three comonomers on the surface with a strong adsorption capacity may compete with propylene for adsorption, which will affect the polymerization. Among them, Vinyltrimethoxysilane, which exhibits the strongest adsorption ability, tends to form bonds with the ethyl on the catalyst surface, leading to catalyst poisoning and inhibiting the reaction. In contrast, 5-hexenyl methyldichlorosilane demonstrates relatively higher activity due to its balanced properties. The order of reactivity in the polymerization reaction: 5-hexenyl methyldichlorosilane > 5-hexenyldichlorophosphonane > vinyltrimethoxysilane. This work provides fundamental mechanistic insights into how functional comonomers interact with catalytic active sites through adsorption, competitive reactions, and insertion processes. Additional free energy analysis at 333 K confirms that these mechanistic trends remain unchanged under realistic reaction conditions. Rather than directly simulating industrial catalysts, the present study focuses on a model TiCl3 system to elucidate intrinsic structure-reactivity relationships. These findings contribute to a deeper understanding of comonomer effects in olefin polymerization at the molecular level. Full article
(This article belongs to the Special Issue Feature Papers in "Industrial Catalysis" Section, 3rd Edition)
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31 pages, 12925 KB  
Article
The Effects of Bisphosphonates Used in Osteoporosis Treatment on Breast Cancer: Analysis with Integrative Bioinformatics Methods, DFT, ADMET and Molecular Docking Analysis
by Sevil Ceyhan Dogan and Kenan Goren
Biology 2026, 15(12), 952; https://doi.org/10.3390/biology15120952 - 18 Jun 2026
Viewed by 448
Abstract
This study evaluated the structural, electronic, pharmacokinetic, and receptor-binding properties of three bisphosphonate derivatives, alendronate, risedronate, and zoledronate, to investigate their therapeutic relevance in osteoporosis and breast cancer. Density Functional Theory (DFT) calculations at the B3LYP/6-31G(d,p) level showed that risedronate exhibited the highest [...] Read more.
This study evaluated the structural, electronic, pharmacokinetic, and receptor-binding properties of three bisphosphonate derivatives, alendronate, risedronate, and zoledronate, to investigate their therapeutic relevance in osteoporosis and breast cancer. Density Functional Theory (DFT) calculations at the B3LYP/6-31G(d,p) level showed that risedronate exhibited the highest kinetic stability (ΔE = 6.7468 eV), whereas zoledronate displayed greater chemical reactivity (ΔE = 2.9669 eV) and the strongest nonlinear optical response (β = 1.20 × 10−30 esu). ADMET analysis indicated acceptable safety profiles for all compounds, although high polarity and low lipophilicity may limit oral bioavailability. Molecular docking against 11 breast cancer- and bone metabolism-related targets revealed favorable binding affinities, particularly for zoledronate and risedronate. Zoledronate showed strong interactions with ESR2, VEGFR/KDR, GGPS1, and FPPS, whereas risedronate exhibited notable affinity for BRCA2 and MMP9. Bioinformatics analyses identified significant dysregulation of GGPS1, FDPS, TNFSF11, ESR1, MMP9, and BRCA2 in breast cancer tissues, while survival analysis linked elevated FDPS, MMP9, and BRCA2 expression to poor prognosis. Network analyses highlighted pathways related to mevalonate metabolism, hormone signaling, angiogenesis, extracellular matrix remodeling, and the RANK/RANKL/OPG axis. These findings support the potential repurposing of bisphosphonates, particularly zoledronate, for breast cancer-associated bone disease. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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22 pages, 6050 KB  
Article
Molecular Modeling of Weakly Caking Coal and the CO2 Inhibition Mechanism of Coal–Oxygen Complexation
by Xiaoyue Zhao, Xihua Zhou and Wenqing Wang
Molecules 2026, 31(12), 2108; https://doi.org/10.3390/molecules31122108 - 15 Jun 2026
Viewed by 255
Abstract
To elucidate the molecular structural characteristics of weakly caking coal and the microscopic mechanism by which CO2 inhibits coal–oxygen complexation, a weakly caking coal sample from the Dahaize coal mine in Shaanxi, China, was investigated using proximate and ultimate analyses, FTIR, XPS, [...] Read more.
To elucidate the molecular structural characteristics of weakly caking coal and the microscopic mechanism by which CO2 inhibits coal–oxygen complexation, a weakly caking coal sample from the Dahaize coal mine in Shaanxi, China, was investigated using proximate and ultimate analyses, FTIR, XPS, and 13C NMR. On this basis, a representative coal macromolecular model was constructed and further analyzed using density functional theory (DFT) and grand canonical Monte Carlo (GCMC) simulations. The molecular formula of the representative weakly caking coal from the Dahaize mine (RNM) unit was determined as C176H156N2O19S2. The aromatic carbon fraction was 65.41%, and the bridge carbon/peripheral carbon ratio was 0.25, indicating a certain degree of aromatic condensation but a limited content of highly fused aromatic structures. DFT calculations revealed that the reactive sites were mainly located around edge oxygen-containing functional groups and bridging structures, with a maximum Fukui index of approximately 0.024. Adsorption simulations showed that O2 and CO2 adsorption on RNM followed Langmuir-type behavior over 303.15–363.15 K: adsorption capacity increased with pressure and decreased with temperature. At 8000 kPa, the CO2 uptake was approximately 1.6 times that of O2. In the binary O2-CO2 system, CO2 preferentially occupied pore surfaces and high-energy adsorption sites, reducing the local enrichment of O2. These results provide a molecular-level explanation for the inhibition of coal–oxygen complexation by CO2 through competitive adsorption, site shielding, and decreased oxidation probability at active sites. Full article
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30 pages, 17440 KB  
Article
AI-Driven Discovery of Prototype CLEC4M Inhibitors Targeting Marburg Virus Entry via Integrated Machine Learning and Molecular Modeling
by Mohammed Almaghrabi and Mansour S. Alturki
Int. J. Mol. Sci. 2026, 27(12), 5324; https://doi.org/10.3390/ijms27125324 - 12 Jun 2026
Viewed by 531
Abstract
Marburg virus (MARV), a highly pathogenic member of the Filoviridae family, causes severe hemorrhagic fever with a high case fatality rate and currently lacks effective therapeutics. The viral entry process, mediated by the interaction between the MARV glycoprotein (GP) and host receptor C-type [...] Read more.
Marburg virus (MARV), a highly pathogenic member of the Filoviridae family, causes severe hemorrhagic fever with a high case fatality rate and currently lacks effective therapeutics. The viral entry process, mediated by the interaction between the MARV glycoprotein (GP) and host receptor C-type lectin domain family 4 member M (CLEC4M) (L-SIGN), represents a critical target for early-stage intervention. The active compounds from BindingDB and the decoy from DUDE were used. The RDKit was used for feature engineering. Machine learning models were trained on an initial dataset consisting of 56 active chemicals and 1232 decoys. Among the tested algorithms, the Random Forest model demonstrated superior performance, achieving the highest discriminative ability (AUC = 0.93, MCC = 0.88) on the test set. Virtual screening of 11,032 phytochemicals resulted in 120 predicted actives, of which 42 compounds satisfied drug-likeness criteria. Subsequent molecular docking identified three lead compounds (PubChem IDs: 42608095, 5281601, and 11243993) with moderate-to-promising binding affinities (−6.3 to −6.5 kcal/mol) toward the CLEC4M binding site. ADMET analysis revealed favorable pharmacokinetic and toxicity profiles for the selected lead compounds. DFT calculations of the three compounds highlighted their electronic stability and reactive nature, indicating that PubChem IDs 42608095 and 5281601 possess particularly stable electronic properties conducive to favorable target interactions. Combining machine learning models with molecular docking and Molecular Dynamics (MD) simulations worked well in finding promising phytochemical inhibitors. The MM/GBSA binding free energy calculations further confirmed binding affinities, with values of −10.83 and −11.08 kcal/mol, respectively, suggesting favorable complex stability. These findings provide a pathway for developing new antiviral agents against MARV, pending further experimental validation and optimization. Full article
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12 pages, 1728 KB  
Short Note
2-Chloro-4,5,6,7-tetrafluoro-2-(methylthio)-1H-indene-1,3(2H)-dione
by Anastasia R. Kovrizhina and Andrei I. Khlebnikov
Molbank 2026, 2026(3), M2189; https://doi.org/10.3390/M2189 - 8 Jun 2026
Viewed by 390
Abstract
We report the synthesis of the new compound 2-chloro-4,5,6,7-tetrafluoro-2-(methylthio)-1H-indene-1,3(2H)-dione (Compound 3), which presents an important type of fluoro-containing heterocycles and is a useful intermediate product in organic synthesis. The structure of the compound was confirmed by the NMR [...] Read more.
We report the synthesis of the new compound 2-chloro-4,5,6,7-tetrafluoro-2-(methylthio)-1H-indene-1,3(2H)-dione (Compound 3), which presents an important type of fluoro-containing heterocycles and is a useful intermediate product in organic synthesis. The structure of the compound was confirmed by the NMR and elemental analysis. A quantum-chemical comparison (DFT) of 2-chloro-2-(methylthio)-1H-indene-1,3(2H)-dione (with C-H bonds, compound 4) and its 4,5,6,7-tetrafluoro derivative (with C-F bonds, compound 3) at the M06-2X/6-311++G(d,p) level in THF showed that the introduction of four fluorine atoms into the benzene ring causes a systematic shortening of the C=O, C-Cl, and C-C bonds of the five-membered ring, as well as an almost twofold decrease in the dipole moment. Replacing hydrogen with fluorine leads to a simultaneous stabilization of the frontier orbitals and a narrowing of the HOMO–LUMO energy gap, while the electron affinity increases by 0.39 eV and the electrophilicity index increases from 2.77 to 3.24 eV, making compound 3 a strong electrophile. Analysis of donor–acceptor interactions (NBOs) and condensed Fukui indices confirms that perfluorination selectively increases the electrophilicity of the sp3-carbon center of C-Cl, making it more susceptible to nucleophilic attack. At the same time, the isodesmic reaction with 1,2,4,5-tetrafluorobenzene yields a positive free energy change (ΔG = +13.4 kcal/mol), indicating that the increased reactivity of compound 3 is kinetic rather than thermodynamic in nature. The synthesized 1,3-indandione derivative thus represents a promising precursor for tetrafluoroninhydrin and can be considered a biologically active compound. Thus, perfluorination of the indandione skeleton is an effective tool for targeted enhancement of electrophilic properties without fundamentally changing the geometry of the molecule, which opens up prospects for the design of new highly reactive reagents. Full article
(This article belongs to the Section Organic Synthesis and Biosynthesis)
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16 pages, 2400 KB  
Article
Molecular Dynamics Study on the Mechanism of Coal High-Temperature Pyrolysis Based on Machine Learning Potential
by Menghao Ren, Rongheng Gou, Hanyu Chen, Tian-Min Wu, Shansong Gao, Dao Li, Haisheng Li, Qing Zheng and Yanjun Zhang
Chemistry 2026, 8(6), 75; https://doi.org/10.3390/chemistry8060075 - 1 Jun 2026
Viewed by 579
Abstract
Understanding the atomic-scale mechanisms of coal pyrolysis is essential for efficient coal utilization and carbon-neutral energy strategies, yet conventional computational approaches often struggle to balance between the high accuracy of quantum-chemical calculations and the efficiency of reactive force fields. To overcome this limitation, [...] Read more.
Understanding the atomic-scale mechanisms of coal pyrolysis is essential for efficient coal utilization and carbon-neutral energy strategies, yet conventional computational approaches often struggle to balance between the high accuracy of quantum-chemical calculations and the efficiency of reactive force fields. To overcome this limitation, we proposed a multiscale computational framework integrating high-throughput density functional theory (DFT) calculations, ReaxFF-based configuration sampling, YARP reaction enumeration, and DPA3-based machine learning potentials (MLPs). Two coal-specific MLPs, DPA3-coal and DPA3-coal@dftb, were constructed and systematically benchmarked on both small molecular systems and larger C20–30 coal fragments extracted from MD simulations. DPA3-coal@dftb model demonstrated significantly improved accuracy over ReaxFF in predicting energies and atomic forces while maintaining good transferability. To balance computational efficiency and accuracy in large-scale simulations, the DPA3-coal model was employed to perform accelerated reactive molecular dynamics simulations of a Solomon-type bituminous coal molecule from 1600 to 2600 K. The simulations revealed temperature-dependent evolution of coke, tar, and gas products, including secondary condensation and deep-cracking processes at elevated temperatures. Higher-level DFT calculations further confirmed the thermodynamic consistency of key reaction pathways involving radical formation, H-transfer, recombination, and CO generation, indicating that coal-specific MLPs provide an effective atomistic tool for investigating mechanistic trends in coal pyrolysis. Full article
(This article belongs to the Special Issue AI and Big Data in Chemistry)
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41 pages, 3622 KB  
Article
Molecular and Functional Interactions Between Cisplatin and Nicotinamide: A Combined Computational, Spectroscopic, and Biological Study
by Beata Szefler, Magdalena Wujak, Agnieszka Skotnicka, Krzysztof Skowron, Julia Czuba, Przemysław Czeleń, Kamil Szupryczyński and Piotr Cysewski
Int. J. Mol. Sci. 2026, 27(11), 4989; https://doi.org/10.3390/ijms27114989 - 30 May 2026
Viewed by 702
Abstract
Cisplatin remains a widely used anticancer agent; however, its effectiveness can be influenced by systemic toxicity, resistance mechanisms, and interactions with exogenous compounds. Nicotinamide (vitamin B3), an NAD+ precursor and a commonly used dietary supplement, is involved in cellular metabolism, redox homeostasis, [...] Read more.
Cisplatin remains a widely used anticancer agent; however, its effectiveness can be influenced by systemic toxicity, resistance mechanisms, and interactions with exogenous compounds. Nicotinamide (vitamin B3), an NAD+ precursor and a commonly used dietary supplement, is involved in cellular metabolism, redox homeostasis, and DNA repair pathways, which may potentially modulate the cellular responses to Platinum-based agents. Here, we combine chemical synthesis, computational studies, spectroscopic analysis, and biological assays to investigate the molecular and biological aspects of Cisplatin–Nicotinamide interactions. A novel cis-[Pt(NH3)2NicotinamideCl]NO3 complex was obtained and its structure analyzed. Density functional theory (DFT) calculations indicate a thermodynamically favorable coordination of Nicotinamide to the first hydrolysis product of Cisplatin (CisPt1) with binding energies comparable to those calculated for nucleobase coordination under the same theoretical conditions. In non-small cell lung cancer cell lines (A549 and PC-9), in vitro results suggest that Nicotinamide pre-treatment reduces Cisplatin cytotoxicity under specific experimental conditions, but the pre-formed complex does not exert anticancer effects. These data are consistent with a model in which Nicotinamide may interact with reactive Cisplatin species, potentially contributing to the reduced availability of reactive Platinum(II) species. This work provides mechanistic insight into potential drug–nutrient interactions involving Platinum-based chemotherapy and highlights the need for further investigation under clinically relevant conditions in the near future. Full article
(This article belongs to the Special Issue Molecular Insights in Biomodelling)
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25 pages, 5177 KB  
Article
Assessment and Density Functional Theory of Bioactive Compounds of Curcuma longa L. Root Responsible for Its Cardio-Protective and Anti-Cancer Activities
by Ahmed Hemdan, Sylvester Nnaemeka Ugariogu, Bashayer D. Althufairi and Naser F. Al-Tannak
Pharmaceuticals 2026, 19(6), 834; https://doi.org/10.3390/ph19060834 - 27 May 2026
Viewed by 1044
Abstract
Background/Objectives: Cardiovascular diseases (CVDs) and cancer remain major global health challenges and are among the leading causes of mortality worldwide, including in Kuwait. Medicinal plants are important sources of bioactive compounds with therapeutic potential. This study aimed to identify the phytochemical constituents of [...] Read more.
Background/Objectives: Cardiovascular diseases (CVDs) and cancer remain major global health challenges and are among the leading causes of mortality worldwide, including in Kuwait. Medicinal plants are important sources of bioactive compounds with therapeutic potential. This study aimed to identify the phytochemical constituents of Curcuma longa L. root extract and evaluate their potential cardioprotective and anticancer activities using integrated computational approaches. Methods: Phytochemical profiling of Curcuma longa root extract was performed using gas chromatography–mass spectrometry (GC–MS). The identified compounds were evaluated through molecular docking against selected cardiovascular- and cancer-related targets, including HMG-CoA reductase, phosphoinositide 3-kinase (PI3K), cyclin-dependent kinase 6 (CDK6), and HER2 kinase receptors. Protein–ligand interactions were analyzed to determine binding stability. Biological activity prediction and pharmacokinetic properties were assessed using PASS prediction and SwissADME tools, while density functional theory (DFT) calculations were conducted to investigate electronic and quantum chemical characteristics associated with ligand reactivity. Results: GC–MS analysis identified seventeen phytochemical constituents with retention times ranging from 7.57 to 32.70 min. The major compounds detected were 2-oxo-cyclooctaneacetic acid (30.88%), curlone (20.99%), and tumerone (13.85%). Molecular docking revealed favorable binding affinities for α-curcumene, caryophyllene, bergamotene, cyclohexene derivatives, tumerone, curlone, and (6R,7R)-bisabolone against the selected targets, with interaction profiles comparable to reference drugs. PASS and SwissADME analyses indicated promising biological activities, acceptable drug-likeness, and favorable pharmacokinetic properties. DFT analysis demonstrated that curlone and tumerone possessed stable electronic configurations and favorable reactivity profiles. Conclusions: The findings suggest that bioactive compounds from Curcuma longa may serve as promising lead candidates for the development of cardioprotective and anticancer agents. However, further experimental validation through in vitro and in vivo studies is required to confirm these computational predictions. Full article
(This article belongs to the Section Natural Products)
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29 pages, 8097 KB  
Article
Identification of GPI-Anchored Wall Transfer Protein 1 Modulators for Fungal Infections Through Generative AI and Physics-Based Approaches
by Ibrahim A. Alsarra, Rupesh Chikhale, Abdullah M. Al-Mohizea and Md Ataul Islam
Int. J. Mol. Sci. 2026, 27(11), 4767; https://doi.org/10.3390/ijms27114767 - 25 May 2026
Viewed by 604
Abstract
Glycosylphosphatidylinositol (GPI) anchored wall transfer protein 1 (GWT1), a fungal-specific inositol acyltransferase, catalyzes the palmitoylation of GlcN-PI in GPI-anchor biosynthesis, crucial for mannoprotein trafficking and attachment, which are vital for cell wall integrity, biofilm formation, and virulence. More than 60,000 AI-generated molecules produced [...] Read more.
Glycosylphosphatidylinositol (GPI) anchored wall transfer protein 1 (GWT1), a fungal-specific inositol acyltransferase, catalyzes the palmitoylation of GlcN-PI in GPI-anchor biosynthesis, crucial for mannoprotein trafficking and attachment, which are vital for cell wall integrity, biofilm formation, and virulence. More than 60,000 AI-generated molecules produced using REINVENT4 were screened using ADMET-AI and GNINA. DeepSA and PharmacoNet were used to select synthesizable and pharmacophorically rich molecules. The dynamic behaviour was explored using molecular dynamics (MD). Finally, molecular reactivity was assessed using density functional theory (DFT). After ADMET filtering, 6190 compounds were docked against GWT1, of which 315 showed better predicted binding energies than the co-crystal ligand. DeepSA identified 105 readily synthesizable candidates, and PharmacoNet retained 32 compounds with favourable pharmacophoric features, from which four final candidates (AF_M1, AF_M2, AF_M3, and AF_M4) were prioritized for further analysis. MD simulation suggested stable binding behavior towards GWT1. DFT analysis indicated favourable electronic properties, low HOMO-LUMO energy gaps, and stable optimized geometries. These molecules could serve as promising lead candidates and potential new therapeutic agents for invasive fungal infections, pending validation. Full article
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22 pages, 4091 KB  
Article
Defect-Engineered Carbon-Spinel Interfaces for Enhanced Periodate Activation for Bisphenol A Degradation
by Bingfei Yan, Haochun Zang, Hao Lu, Haibo Li and Bin Li
Water 2026, 18(11), 1262; https://doi.org/10.3390/w18111262 - 23 May 2026
Viewed by 745
Abstract
Developing efficient and sustainable catalysts for advanced oxidation processes (AOPs) to remove endocrine-disrupting compounds remains a critical challenge. In this study, a defect-engineered MnFe2O4@SBC composite was synthesized by loading spinel MnFe2O4 onto sewage sludge-derived biochar (SBC) [...] Read more.
Developing efficient and sustainable catalysts for advanced oxidation processes (AOPs) to remove endocrine-disrupting compounds remains a critical challenge. In this study, a defect-engineered MnFe2O4@SBC composite was synthesized by loading spinel MnFe2O4 onto sewage sludge-derived biochar (SBC) prepared at different calcination temperatures, and applied for efficient periodate (PI) activation toward bisphenol A (BPA) degradation. The catalytic performance exhibited a volcano-type dependence on calcination temperature, with MnFe2O4@SBC-750 achieving the highest BPA removal efficiency (98.6% within 30 min). Structural characterization revealed that MnFe2O4@SBC-750 possessed an optimized carbon structure with a balance between defect sites and graphitized domains. Mechanistic investigations demonstrated that multiple reactive oxygen species, including OH, O2•−, IO3 and 1O2, were involved in BPA degradation. LC-MS analysis identified key transformation intermediates and proposed degradation pathways, while toxicity assessment confirmed reduced ecological risks after treatment. Density functional theory (DFT) calculations indicated that MnFe2O4@SBC significantly enhanced PI adsorption and activation by promoting interfacial electron transfer and elongating the I-O bond in IO4. Notably, MnFe2O4@SBC-750 exhibited the strongest electron transfer capability, attributed to the optimal regulation of defect density and graphitization degree, which facilitated π-d electronic coupling at the MnFe2O4-SBC interface. Overall, this work elucidates the critical role of defect regulation in spinel biochar-based catalysts for oxidant activation and provides a sustainable strategy for converting sewage sludge into high-performance catalysts for water purification. Full article
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