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Chemistry, Volume 8, Issue 3 (March 2026) – 8 articles

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17 pages, 2248 KB  
Article
In Silico Identification of Hit Compound to Counteract A-Series Nerve Agents Poisoning
by Nikola Maraković
Chemistry 2026, 8(3), 37; https://doi.org/10.3390/chemistry8030037 - 23 Mar 2026
Viewed by 256
Abstract
Organophosphorus (OP) nerve agents inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) by phosphylating the catalytic serine. Oxime reactivators can restore enzymatic activity by a nucleophilic attack of the oximate anion on the phosphorus center of the enzyme–OP conjugate; however, clinically used oximes show agent- [...] Read more.
Organophosphorus (OP) nerve agents inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) by phosphylating the catalytic serine. Oxime reactivators can restore enzymatic activity by a nucleophilic attack of the oximate anion on the phosphorus center of the enzyme–OP conjugate; however, clinically used oximes show agent- and enzyme-dependent performance and are particularly challenged by A-series compounds. Here, an in silico strategy is presented to identify candidate antidotes for OP poisoning, including A-series agents. Pharmacophore models are generated from benchmark/template oximes. Pharmacophore-based virtual screening is used to retrieve hit-like scaffolds from the available chemical space, after which selected hits are converted into oxime analogs. Template oximes and newly designed oximes are then docked into the active site of AChE or BChE inhibited by specific nerve agents. The predicted reactivation potential is assessed using mechanistically motivated geometric criteria derived from the accepted reactivation hypothesis, including the distance between the oximate oxygen and the phosphyl phosphorus and the attack angle, relative to the catalytic serine Oγ. This workflow enables a controlled, pairwise comparison of new oximes against their corresponding template oximes for each enzyme–agent combination, providing a rational basis for prioritizing candidates for synthesis and experimental validation. Using the described workflow, we identified a hit compound with the potential to act as an antidote against A-series nerve agent A-230 poisoning. Full article
(This article belongs to the Section Medicinal Chemistry)
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11 pages, 1678 KB  
Article
Ratiometric Fluorescent Detection of Carbaryl Based on Molecular Intrinsic Fluorescence Enhancement and Gold Nanoclusters
by Xiujin Chen, Jingyang Jiang, Xiufang Huang and Chifang Peng
Chemistry 2026, 8(3), 36; https://doi.org/10.3390/chemistry8030036 - 19 Mar 2026
Viewed by 204
Abstract
In this work, a ratiometric fluorescent method for carbaryl detection is reported. We found that the combination of rapid hydrolysis of carbaryl and cetyltrimethylammonium bromide (CTAB) emulsification could significantly enhance the intrinsic weak blue fluorescence of carbaryl. By using red fluorescent glutathione-gold nanoculsters [...] Read more.
In this work, a ratiometric fluorescent method for carbaryl detection is reported. We found that the combination of rapid hydrolysis of carbaryl and cetyltrimethylammonium bromide (CTAB) emulsification could significantly enhance the intrinsic weak blue fluorescence of carbaryl. By using red fluorescent glutathione-gold nanoculsters (GSH-Au NCs) as a reference signal, ratiometric detection of carbaryl within 3 min was successfully achieved. The method exhibited high sensitivity, with a linear response to carbaryl in the range from 1.0 to 70 ng/mL and an LOD of 0.05 ng/mL. The method was applied for detection of carbaryl in apple and cabbage samples, and recovery rates of 90~101% and 93~110%, respectively, were obtained. These results show that the proposed method for carbaryl detection has great potential for application in food sample monitoring. Full article
(This article belongs to the Special Issue Fluorescent Chemosensors and Probes for Detection and Imaging)
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15 pages, 3087 KB  
Article
Synthesis of Macroporous Carbon Adsorbent for Effective Bacterial Removal from Water
by Ivanka Stoycheva, Petar Petrov, Bilyana Petrova, Boyko Tsyntsarski, Angelina Kosateva, Lyudmila Velkova, Nartzislav Petrov, Pavlina Dolashka and Jugoslav Krstić
Chemistry 2026, 8(3), 35; https://doi.org/10.3390/chemistry8030035 - 16 Mar 2026
Viewed by 286
Abstract
Water purification by adsorption of various pollutants using carbon adsorbents with different characteristics has proven to be an effective method that is often used in purification technologies. In this work, a new method for obtaining a carbon adsorbent with a wide pore size [...] Read more.
Water purification by adsorption of various pollutants using carbon adsorbents with different characteristics has proven to be an effective method that is often used in purification technologies. In this work, a new method for obtaining a carbon adsorbent with a wide pore size and high surface area has been developed, particularly for the adsorption of bacterial cells. The characterization of the porous texture, the chemical nature of the surface, the structure, and the chemical composition of the obtained adsorbent is studied. The study demonstrates that the hierarchical macroporous structure of the macroporous carbon adsorbent (MCA) is highly effective for the physical sequestration of Escherichia coli from aqueous solutions. The high removal efficiency (86.4%) suggests that this material is a promising candidate for water purification and point-of-use filtration systems, where physical immobilization of pathogens is required. Full article
(This article belongs to the Section Green and Environmental Chemistry)
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24 pages, 4754 KB  
Article
Atomic Charges from Machine-Learned Charge Densities: Consistency and Substituent Effects
by Xuejian Qin and Taoyuze Lv
Chemistry 2026, 8(3), 34; https://doi.org/10.3390/chemistry8030034 - 16 Mar 2026
Viewed by 330
Abstract
Atomic charges are widely used to analyze molecular electronic structure and substituent effects, yet their numerical values and interpretations are inherently dependent on the adopted density partitioning scheme. Here, we adapt the Equivariant Atomic Contribution framework to molecular systems (EAC-qm), enabling prediction of [...] Read more.
Atomic charges are widely used to analyze molecular electronic structure and substituent effects, yet their numerical values and interpretations are inherently dependent on the adopted density partitioning scheme. Here, we adapt the Equivariant Atomic Contribution framework to molecular systems (EAC-qm), enabling prediction of atom-resolved continuous charge densities from which atomic charges are obtained as spatial moments. The predicted densities reproduce reference density functional theory results with high accuracy and preserve global charge conservation. To assess chemical interpretability, we examine charge responses in monosubstituted aromatic systems using Hammett substituent constants as external empirical references. Atomic charges derived from EAC-qm exhibit a strong linear association with Hammett parameters, compared with values obtained from traditional density partitioning approaches applied to the same electronic structures. These correlations indicate that density-derived charges respond systematically to established substituent electronic trends. Beyond scalar charges, atom-resolved dipole moments can be evaluated as first-order moments of the same continuous density representation. Illustrative examples for formaldehyde (H2CO) and formamide (HCONH2) show that local dipole vectors provide directional information about intra-atomic polarization that is not captured by point-charge models. Overall, the results suggest that machine-learned continuous electron densities provide a representation-consistent basis for constructing atom-centered electronic descriptors with chemical interpretability. Full article
(This article belongs to the Section Theoretical and Computational Chemistry)
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13 pages, 1138 KB  
Article
Effects of Vibrationally Treated Aqueous Media on the Kinetics of Methylene Blue Reduction by Ascorbic Acid
by Natalia Rodionova, Evgenia Nechaeva, German Stepanov, Anastasia Petrova and Sergey Tarasov
Chemistry 2026, 8(3), 33; https://doi.org/10.3390/chemistry8030033 - 3 Mar 2026
Viewed by 634
Abstract
As a primary reaction medium, water profoundly influences the kinetics and mechanisms of chemical processes. External physical treatments, such as vibration, can alter the physicochemical properties of water, thereby modifying reaction outcomes. This study aimed to investigate the effect of vibrational iterations (I0–I7) [...] Read more.
As a primary reaction medium, water profoundly influences the kinetics and mechanisms of chemical processes. External physical treatments, such as vibration, can alter the physicochemical properties of water, thereby modifying reaction outcomes. This study aimed to investigate the effect of vibrational iterations (I0–I7) prepared using the “crossing” technology on the kinetics of the oxidation–reduction reaction between methylene blue and ascorbic acid, a standard model for evaluating external influences. Initial characterization revealed that while pH remained stable across all samples, electrical conductivity and dissolved oxygen levels deviated significantly from the control (intact water), with oxygen concentrations measuring either higher or lower than the control. Following the dissolution of methylene blue in these iterations, absorption spectroscopy was used to monitor decolorization kinetics. Different vibrational iterations influenced distinct kinetic parameters, including the rate constant, half-reaction time, and average reaction rate. Depending on the number of processing steps used to prepare the iterations, these parameters exhibited deviations ranging from 3% to 9% compared to the control. This suggests a complex relationship between the aqueous medium’s structural–dynamic properties and the reactants’ supramolecular organization. These findings underscore the potential of vibrational iterations as a tool for modulating chemical reaction kinetics through aqueous medium engineering. Further research is needed to elucidate the underlying mechanisms and expand the applicability of this approach to other systems. Full article
(This article belongs to the Section Physical Chemistry and Chemical Physics)
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27 pages, 1917 KB  
Article
Machine Learning and Approximated Estimation Approaches for Process Design in Drug Synthesis
by Andrea Repetto, Gianguido Ramis and Ilenia Rossetti
Chemistry 2026, 8(3), 32; https://doi.org/10.3390/chemistry8030032 - 3 Mar 2026
Viewed by 646
Abstract
The continuous-flow technologies in organic synthesis for the production of active pharmaceutical ingredients (APIs) are nowadays more and more applied. In-silico process design is a powerful tool able to support organic synthesis in the field of scale-up and process development. Process design feasibility [...] Read more.
The continuous-flow technologies in organic synthesis for the production of active pharmaceutical ingredients (APIs) are nowadays more and more applied. In-silico process design is a powerful tool able to support organic synthesis in the field of scale-up and process development. Process design feasibility and reliability depend on the availability of a well-defined chemical reaction kinetic scheme, information which is usually derived from experimental datasets collected on purpose. The latter approach is time-consuming and demanding in terms of resources. Different possibilities are here proposed to valorize widely available experimental data from explorative works with different approaches, depending on the nature, richness, and structure of the datasets. The kinetic parameters (i.e., reaction order, kinetic constant, and activation energy) of some interesting organic reactions have been approximately estimated by applying different computational methodologies, thanks to built-in experimental databases. The numerical algebra approach dealing with linear and non-linear regression analysis for the kinetic parameters has been initially considered and related to the database information for oseltamivir synthesis. The Bayesian statistic was applied to the ibuprofen case through the application of the Markov Chain Monte Carlo (MCMC) method for reaction order estimation. At last, a Machine Learning (ML) approach has been applied to the Rolipram and Pregabalin case study. The in-house developed T-ReX experimental kinetic constant database was exploited, with application of the k-Nearest neighbor algorithm for classification and regular expression pattern recognition. Advantages and limitations of the three approaches are discussed. Full article
(This article belongs to the Special Issue AI and Big Data in Chemistry)
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43 pages, 1959 KB  
Review
Advances in Photodynamic Therapy: Photosensitizers, Biological Mechanisms, and Artificial Intelligence-Driven Innovation
by Jadwiga Inglot, Dorota Bartusik-Aebisher, Katarzyna Bania, Klaudia Dynarowicz and David Aebisher
Chemistry 2026, 8(3), 31; https://doi.org/10.3390/chemistry8030031 - 2 Mar 2026
Viewed by 1160
Abstract
Photodynamic therapy (PDT) is a minimally invasive therapeutic modality that combines a photosensitizer, light of an appropriate wavelength, and molecular oxygen to generate cytotoxic reactive oxygen species for selective tissue destruction. Over recent decades, PDT has evolved from early porphyrin-based systems to advanced [...] Read more.
Photodynamic therapy (PDT) is a minimally invasive therapeutic modality that combines a photosensitizer, light of an appropriate wavelength, and molecular oxygen to generate cytotoxic reactive oxygen species for selective tissue destruction. Over recent decades, PDT has evolved from early porphyrin-based systems to advanced third-generation photosensitizers incorporating nanotechnology, targeting ligands, and activatable designs, significantly improving tumor selectivity, pharmacokinetics, and therapeutic efficacy. This article offers an in-depth look at the fundamental principles of PDT, including the roles of photosensitizers, light delivery systems, and oxygen dynamics, as well as the resulting biological effects such as direct tumor cell death, vascular shutdown, and immune activation. Clinical applications across oncology, dermatology, ophthalmology, and antimicrobial therapy are discussed, highlighting both established and emerging indications. Furthermore, the review critically examines recent advances in machine learning (ML) and deep learning (DL) applied to PDT, including treatment planning, dosimetry optimization, photosensitizer and nanoparticle design, real-time treatment monitoring, and outcome prediction. By integrating physics-based modeling, multimodal imaging, and artificial intelligence-driven approaches, PDT is transitioning toward adaptive, personalized photomedicine. This work outlines current challenges, future research directions, and the translational potential of AI-enabled PDT systems, emphasizing their role in improving precision, reproducibility, and clinical outcomes. Full article
(This article belongs to the Special Issue Modern Photochemistry and Molecular Photonics)
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17 pages, 4976 KB  
Article
A Dual-Passivation Strategy to Enhance Exciton Luminescence and Bimodal Anticounterfeiting in Red Perovskite Quantum Dots
by Keyujia Zhong, Fang Lei, Shiqing Dang, Hongyang Zhang, Ying Shi and Haohong Chen
Chemistry 2026, 8(3), 30; https://doi.org/10.3390/chemistry8030030 - 26 Feb 2026
Viewed by 542
Abstract
Perovskite quantum dots (PQDs) face significant performance limitations due to surface defects, which are not sufficiently addressed by conventional single-passivation methods. We introduce a dual-passivation strategy that synergistically combines bifunctional ligand 3-(N,N-dimethyloctadecylammonium)-propanesulfonate (SB3-18) treatment with silica coating to simultaneously passivate undercoordinated Pb2+ [...] Read more.
Perovskite quantum dots (PQDs) face significant performance limitations due to surface defects, which are not sufficiently addressed by conventional single-passivation methods. We introduce a dual-passivation strategy that synergistically combines bifunctional ligand 3-(N,N-dimethyloctadecylammonium)-propanesulfonate (SB3-18) treatment with silica coating to simultaneously passivate undercoordinated Pb2+ ions and bromine vacancies in red-emitting CsPb(Br/I)3 PQDs. This approach nearly triples the photoluminescence quantum yield (PLQY, from 23% to 58%). Systematic structural, morphlogical, binding energy, Fermi level and optical analyses confirm effective defect suppression and enhanced exciton luminescence. The dual-passivated sample QDs:SB3-18@SiO2 also exhibit excellent environmental stability, retaining 85% of their initial emission after 30 min in air and exhibiting improved UV resistance. By combining the PQDs with a CGSO:Tb3+ mechanoluminescent phosphor, a composite film is fabricated with bimodal optical response—color-selective photoluminescence under UV excitation and stress-activated green emission upon scratching. This work presents a robust route to high-performance PQDs and demonstrates their potential for advanced anticounterfeiting and smart optical applications. Full article
(This article belongs to the Section Chemistry of Materials)
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