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Organics, Volume 6, Issue 1 (March 2025) – 12 articles

Cover Story (view full-size image): Bacterial 16S rRNA DNA acts as a nano-sized information archive, characterising soil microbial communities. It reveals both recent ecological conditions and past human impacts, aiding archaeology and understanding historical ecological effects. Advanced sequencing methods, like Illumina, enable the efficient analysis of soil bacterial composition in topsoil and archaeological sites (e.g., settlements, burials). This overview highlights recent developments in using these molecular nano-archives to study archaeological soil samples, with typical examples illustrated. View this paper
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13 pages, 4529 KiB  
Article
Graft Reaction of Furfural with Polyvinyl Chloride and Its Effect on Thermal Stability of Polyvinyl Chloride
by Mengying Kou and Kanshe Li
Organics 2025, 6(1), 12; https://doi.org/10.3390/org6010012 - 4 Mar 2025
Viewed by 542
Abstract
A graft reaction of polyvinyl chloride (PVC) with furfural was conducted in a tetrahydrofuran solution. The resulting graft structure (FF-g-PVC) was characterized using UV spectroscopy, photoluminescence (PL), Fourier Transform Infrared (FTIR) spectroscopy, Raman spectroscopy, and proton nuclear magnetic resonance (1H NMR) [...] Read more.
A graft reaction of polyvinyl chloride (PVC) with furfural was conducted in a tetrahydrofuran solution. The resulting graft structure (FF-g-PVC) was characterized using UV spectroscopy, photoluminescence (PL), Fourier Transform Infrared (FTIR) spectroscopy, Raman spectroscopy, and proton nuclear magnetic resonance (1H NMR) spectroscopy. The grafting efficiency was determined through ultraviolet spectrophotometry. Thermal stability analysis via thermogravimetric (TG) testing revealed that furfural was successfully grafted onto the PVC chain. In a nitrogen atmosphere, the temperature of the maximum weight loss rate during the first stage of pyrolysis increased from 296.3 °C to 301.7 °C, while the activation energy for the second stage increased from 199.4 kJ/mol to 294.4 kJ/mol, indicating enhanced stability and delayed degradation of the PVC. Additionally, microwave irradiation markedly improved the graft reaction, achieving a grafting rate of 57.76‰ compared to only 1.808‰ with water bath heating. The optimal conditions were found to be a PVC/FF/Zn ratio of 1:1:0.9, with microwave irradiation for 20 min at 40 °C. Full article
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14 pages, 9759 KiB  
Article
Synthesis and Biological Evaluation of Salicylaldehyde-Derived Secondary Amines: Antioxidant, Anti-Inflammatory, and Insecticidal Activities with DFT Insights
by Chamseddine Derabli, Noureddine Rahim, Roumaissa Djaba, Sarra Aouidi, Chawki Bensouici, Stephanie Hesse and Houssem Boulebd
Organics 2025, 6(1), 11; https://doi.org/10.3390/org6010011 - 3 Mar 2025
Viewed by 533
Abstract
Six secondary amine derivatives derived from salicylaldehyde (SA) were successfully synthesized in good to excellent yields and evaluated for their biological activities. The synthesized compounds exhibited remarkable antioxidant properties, as determined by ABTS and phenanthroline assays. Notably, compound 2 demonstrated an IC50 [...] Read more.
Six secondary amine derivatives derived from salicylaldehyde (SA) were successfully synthesized in good to excellent yields and evaluated for their biological activities. The synthesized compounds exhibited remarkable antioxidant properties, as determined by ABTS and phenanthroline assays. Notably, compound 2 demonstrated an IC50 value of 5.14 ± 0.11 µM in the ABTS assay, approximately six to nine times lower than the standards BHT and BHA. In the phenanthroline assay, all compounds showed inhibition capacities five to ten times greater than BHT and comparable to BHA, with A0.5 values ranging from 9.42 to 31.73 µM. Among these, compound 5 displayed the lowest A0.5 value of 9.42 ± 1.02 µM. The anti-inflammatory activity, assessed through BSA denaturation, revealed that compounds 2 and 5 were the most promising, although their activity was moderate compared to the standard diclofenac. The insecticidal potential of the compounds was evaluated against the storage insect pest Tribolium castaneum. Among the tested derivatives, compounds 1 and 6 exhibited the highest efficacy, achieving maximum mortality rates of 73.31% and 76.67%, respectively, over a seven-day treatment period. Furthermore, the molecular geometry, electronic properties, and intramolecular interactions of all compounds were investigated using DFT calculations. Thermodynamic analyses of the antioxidant mechanisms suggested that the NH bond is the most likely site for free radical attacks. These findings underscore the significant biological potential of the synthesized salicylaldehyde-derived secondary amines. Full article
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16 pages, 3593 KiB  
Article
Luminescence of the Conjugate Bases of [2-(2-Hydroxyphenyl)phenyl]phosphinic Acid and Single-Crystal X-Ray Structure Determination of Sodium [2-(2-Hydroxyphenyl)phenyl]phosphinate
by Valeria Gagliardi, Jesús Castro, Valentina Beghetto, María Expósito and Marco Bortoluzzi
Organics 2025, 6(1), 10; https://doi.org/10.3390/org6010010 - 3 Mar 2025
Viewed by 461
Abstract
The commercial flame-retardant 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) was almost quantitatively converted in sodium [2-(2-hydroxyphenyl)phenyl]phosphinate Na[OH-Ph-Ph-PHO2] and disodium 2-(2-phosphinatophenyl)benzen-1-olate Na2[O-Ph-Ph-PHO2] under mild reaction conditions and without the use of toxic reactants. The structure of Na[OH-Ph-Ph-PHO2] was determined by [...] Read more.
The commercial flame-retardant 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) was almost quantitatively converted in sodium [2-(2-hydroxyphenyl)phenyl]phosphinate Na[OH-Ph-Ph-PHO2] and disodium 2-(2-phosphinatophenyl)benzen-1-olate Na2[O-Ph-Ph-PHO2] under mild reaction conditions and without the use of toxic reactants. The structure of Na[OH-Ph-Ph-PHO2] was determined by means of single-crystal X-ray diffraction. The inter- and intramolecular Na-O interactions generate a stair-like framework where the sodium cations are five-coordinated and exhibit a highly distorted coordination sphere. The two compounds are characterized by appreciable blue luminescence at the solid state upon excitation with UV light, attributed to S1→S0 decays on the basis of time-resolved measurements and computational calculations. The photoluminescence quantum yield is higher for Na2[O-Ph-Ph-PHO2], and the emission and excitation bands are shifted at longer wavelengths. The disodium salt showed affinity towards cellulose, and doped Na2[O-Ph-Ph-PHO2]@cellulose samples maintained emission features comparable to those of the pure compound. The nature of the interaction between cellulose and the emitting species was studied by means of periodic density functional theory calculations, that highlighted the role of the sodium cations. Full article
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11 pages, 2298 KiB  
Article
Photochemical Acylation of 1,4-Naphthoquinone with Aldehydes Under Continuous-Flow Conditions
by Madyan A. Yaseen and Michael Oelgemöller
Organics 2025, 6(1), 9; https://doi.org/10.3390/org6010009 - 14 Feb 2025
Viewed by 590
Abstract
A series of photoacylations of 1,4-naphthoquinone with various aldehydes and using Pyrex-filtered UVB light was conducted under continuous-flow conditions. Acetone served as a triplet photosensitizer and convenient solvent that kept all materials in solution and could be easily removed. The corresponding acylated 1,4-naphthohydroquinone [...] Read more.
A series of photoacylations of 1,4-naphthoquinone with various aldehydes and using Pyrex-filtered UVB light was conducted under continuous-flow conditions. Acetone served as a triplet photosensitizer and convenient solvent that kept all materials in solution and could be easily removed. The corresponding acylated 1,4-naphthohydroquinone photoproducts were obtained in acceptable to excellent yields of 30–90% with residence times of just 70 min. The photoacylation process was successfully coupled with in-line oxidation to obtain acylated 1,4-naphthoquinones. Full article
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18 pages, 4225 KiB  
Article
Synthesis and Characterization of the Conjugated Peptide Lunatin-Folate
by Amanda Neves de Souza, Adriano Monteiro de Castro Pimenta and Rodrigo Moreira Verly
Organics 2025, 6(1), 8; https://doi.org/10.3390/org6010008 - 11 Feb 2025
Viewed by 623
Abstract
Bioactive peptides are promising therapeutic agents due to their antimicrobial and anticancer activities, although their lack of selectivity often limits clinical applications. This study demonstrates the optimal synthetic route for conjugating folic acid (FA) with the bioactive peptide Lunatin-1, aiming to improve selectivity [...] Read more.
Bioactive peptides are promising therapeutic agents due to their antimicrobial and anticancer activities, although their lack of selectivity often limits clinical applications. This study demonstrates the optimal synthetic route for conjugating folic acid (FA) with the bioactive peptide Lunatin-1, aiming to improve selectivity for neoplastic cells. The synthesis combines solid-phase peptide synthesis (SPPS) and Cu(I)-catalyzed cycloaddition to link folic acid to Lunatin-1 via a triazole ring. Using the model tripeptide FIG-NH2, key intermediates and the final product were characterized by high-performance liquid chromatography (HPLC), mass spectrometry (MALDI-ToF), Fourier-transform infrared spectroscopy (FTIR), and nuclear magnetic resonance (NMR). Reaction yields and purity were optimized with FIG-NH2, providing a reproducible synthesis pathway. Additionally, the results confirmed successful conjugation, with the FA-Trz-Luna product exhibiting molecular integrity and structural stability, as validated by spectral analyses. This study highlights a potential synthesis route for peptide-folate conjugates to be used as selective and multifunctional therapeutic agents, laying the groundwork for biological evaluations of their cytotoxicity and antimicrobial properties. Full article
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16 pages, 2219 KiB  
Article
Synthesis of Bispidine-Based Prostate-Specific Membrane Antigen-Targeted Conjugate and Initial Investigations
by Aleksei E. Machulkin, Stanislav A. Petrov, Maria D. Kraynova, Anastasiia S. Garanina, Bayirta V. Egorova, Roman V. Timoshenko, Alexander N. Vaneev, Alexander S. Erofeev, Anna B. Priselkova, Mikhail A. Kalinin, Aleksei V. Medved′ko, Stepan N. Kalmykov, Elena K. Beloglazkina and Sergey Z. Vatsadze
Organics 2025, 6(1), 7; https://doi.org/10.3390/org6010007 - 10 Feb 2025
Viewed by 695
Abstract
Nowadays, PSMA ligands are widely used for radiotheragnostic purposes in prostate cancer. The synthesis of a PSMA-Bisp conjugate was developed and realized with good yield (overall yield ~58% for the last two steps). All newly synthesized compounds were characterized by physicochemical methods: 1 [...] Read more.
Nowadays, PSMA ligands are widely used for radiotheragnostic purposes in prostate cancer. The synthesis of a PSMA-Bisp conjugate was developed and realized with good yield (overall yield ~58% for the last two steps). All newly synthesized compounds were characterized by physicochemical methods: 1H and 13C NMR, HRMS, and LCMS (for biologically tested samples). Subsequently, Bisp1 (diacetate bispidine ligand), Bisp-alkyne (bifunctional derivative of Bisp1), and its conjugate PSMA-Bisp were labeled by 64Cu in mild conditions. In vitro studies of the labeled conjugate [64Cu]Cu-PSMA-Bisp have shown great stability in model solutions. Finally, [64Cu]Cu-PSMA-Bisp was compared to the well-known PSMA-617 conjugate labeled with 64Cu and they showed similar stability in excess bovine serum (BVS), and at the same time, labeling PSMA-Bisp with 64Cu is characterized by extremely high kinetics in mild conditions, while labeling PSMA-617 with 64Cu requires heating (90 °C). Thus, this conjugate can be incredibly promising for nuclear medicine. Full article
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11 pages, 2180 KiB  
Article
Facile Synthesis of a Cholesterol–Doxorubicin Conjugate Using Cholesteryl-4-nitrophenolate as an Activated Ester and Biological Property Analysis
by Pedro Freitas, Dina Maciel, Jolanta Jaśkowska, Kamila Zeńczak-Tomera, Yanbiao Zhou, Guoyin Yin and Ruilong Sheng
Organics 2025, 6(1), 6; https://doi.org/10.3390/org6010006 - 9 Feb 2025
Viewed by 785
Abstract
Developing new biomolecule–drug conjugates as prodrugs is a promising area for natural products and pharmaceutical chemistry. Herein, a cholesterol–doxorubicin (Chol-DOX) conjugate was synthesized using cholesteryl-4-nitrophenolate as a facile, stable, and controllable activated ester. This approach offers an alternative to the conventional HCl-emitting cholesteryl [...] Read more.
Developing new biomolecule–drug conjugates as prodrugs is a promising area for natural products and pharmaceutical chemistry. Herein, a cholesterol–doxorubicin (Chol-DOX) conjugate was synthesized using cholesteryl-4-nitrophenolate as a facile, stable, and controllable activated ester. This approach offers an alternative to the conventional HCl-emitting cholesteryl chloroformate method. Semi-empirical theoretical calculations showed that cholesteryl-4-nitrophenolate exhibits moderate reactivity, greater thermodynamic stability, a higher dipole moment, and a lower HOMO-LUMO energy gap compared to cholesteryl chloroformate, suggesting that cholesteryl-4-nitrophenolate could be used as a more controllable acylating agent. The structure of the synthesized Chol-DOX conjugate was characterized using NMR, MS, and FT-IR techniques. Biological properties of the Chol-DOX conjugate were analyzed with a comparison of theoretical and experimental data. This work provides a facile and controllable method to synthesize natural lipid–DOX prodrugs and offers an in-depth data analysis of the related biological properties. Full article
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11 pages, 1336 KiB  
Article
Vinylation of Alcohols, Thiols, and Nitrogen Compounds Using a Stoichiometric Amount of In Situ Generated Acetylene
by Maria S. Ledovskaya, Vladimir V. Voronin, Anna A. Reznichenko and Ekaterina A. Reznichenko
Organics 2025, 6(1), 5; https://doi.org/10.3390/org6010005 - 8 Feb 2025
Viewed by 1040
Abstract
In this work, we developed a highly efficient and versatile environmentally benign methodology for the vinylation of a broad scope of substances, including alcohols, thiols, and nitrogen compounds. The key advantage of the proposed method is the use of calcium carbide as a [...] Read more.
In this work, we developed a highly efficient and versatile environmentally benign methodology for the vinylation of a broad scope of substances, including alcohols, thiols, and nitrogen compounds. The key advantage of the proposed method is the use of calcium carbide as a robust acetylene source in a stoichiometric ratio to the substrates. Lacking the requirement of acetylene excess, the developed protocol is safe, highly economic, and limits waste production. The procedure allows for a large variety of O-,S-,N-vinyl compounds to be synthesized in up to quantitative yields. Our methodology is scalable, allowing us to obtain vinyl derivatives in Gram-scale quantities. We also demonstrated the significant synthetic value of our approach by performing a label-economic synthesis of 13C2-labeled vinyl derivatives using calcium carbide-13C2. In our well-optimized process, the conversion of Ca13C2 reached 89%. Full article
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17 pages, 2664 KiB  
Review
Ferrocene Derivatives as Histone Deacetylase Inhibitors: Synthesis and Biological Evaluation
by Rostislava Angelova and Georgi Stavrakov
Organics 2025, 6(1), 4; https://doi.org/10.3390/org6010004 - 26 Jan 2025
Viewed by 939
Abstract
Ferrocene is an organometallic compound that has attracted considerable scientific interest due to its unique properties, including low toxicity, excellent stability in aqueous and aerobic media, and high lipophilicity, which enhances membrane permeability. The ferrocene moiety has been effectively used as a bioisostere [...] Read more.
Ferrocene is an organometallic compound that has attracted considerable scientific interest due to its unique properties, including low toxicity, excellent stability in aqueous and aerobic media, and high lipophilicity, which enhances membrane permeability. The ferrocene moiety has been effectively used as a bioisostere of phenyl rings and heteroaromatic groups in the structures of approved tyrosine kinase inhibitors and histone deacetylase inhibitors (HDACis). HDACis exert their cytotoxic effects by blocking cyclin/CDK complexes, causing cell cycle arrest, inducing apoptosis, inhibiting angiogenesis, and through non-histone-directed mechanisms. This mini-review summarizes the synthesis and biological evaluation of small libraries of compounds in which a ferrocenyl moiety is incorporated into the structure of suberoylanilide hydroxamic acid (SAHA) and a number of analogues. The influence of the organometallic function on the antiproliferative effect is investigated. Both docking analysis and in vitro studies confirm that the ferrocenyl-modified HDACis exhibit potent cytotoxicity and strong inhibitory activity against the various enzyme isoforms. Full article
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16 pages, 2321 KiB  
Review
Synthesis and Pharmacology of Clinical Drugs Containing Isoindoline Heterocycle Core
by Mukund Jha, Dani Youssef, Haley Sheehy and Amitabh Jha
Organics 2025, 6(1), 3; https://doi.org/10.3390/org6010003 - 14 Jan 2025
Cited by 1 | Viewed by 1140
Abstract
Heterocyclic compounds are the cornerstone for active pharmaceutical ingredients. Among heterocycles, isoindoline core occupies a special place, as ten commercial bioactive compounds/drugs contain this skeleton decorated with several functional groups required for optimal receptor binding. These drugs are employed for indications such as [...] Read more.
Heterocyclic compounds are the cornerstone for active pharmaceutical ingredients. Among heterocycles, isoindoline core occupies a special place, as ten commercial bioactive compounds/drugs contain this skeleton decorated with several functional groups required for optimal receptor binding. These drugs are employed for indications such as multiple myeloma, leukemia, inflammation, hypertension, edema, obesity, and insect control. This review presents the pharmacological activities, mechanisms of action, and chemical syntheses of these commercial bioactive molecules/drugs. Full article
(This article belongs to the Special Issue Chemistry of Heterocyclic Compounds)
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11 pages, 1112 KiB  
Article
Protolytic Equilibria of Cetirizine in the Presence of Micelle-Forming Surfactants
by Marija Popović-Nikolić, Gordana Popović, Slavica Oljačić and Katarina Nikolić
Organics 2025, 6(1), 2; https://doi.org/10.3390/org6010002 - 2 Jan 2025
Viewed by 850
Abstract
The acid–base equilibria of cetirizine were investigated with and without the presence of differently charged micelle-forming surfactants (anionic, cationic, nonionic). The pKa values were potentiometrically determined at 25 °C and at a constant ionic strength (0.1 M NaCl). Experimental data were [...] Read more.
The acid–base equilibria of cetirizine were investigated with and without the presence of differently charged micelle-forming surfactants (anionic, cationic, nonionic). The pKa values were potentiometrically determined at 25 °C and at a constant ionic strength (0.1 M NaCl). Experimental data were analyzed by applying the computer program Hyperquad 5.2.15. Based on a shift in the ionization constants (∆pKa) in micellar solutions against the pKa values determined in “pure” water under the same conditions, the effects of micelles on the protolytic equilibria of cetirizine were estimated. Applied micelles caused a shift in the protolytic equilibria of all cetirizine ionizable centers, with the piperazine function connected to aliphatic side moiety (∆pKa1 from −0.47 to +1.42), carboxyl group (∆pKa2 from −0.92 to +2.02), and piperazine nitrogen connected to phenyl rings (∆pKa3 from −2.01 to +2.19). Anionic SDS and nonionic Brij 35 micelles caused an increase in the pKa values of the ionizable centers of cetirizine, while a decrease in the pKa values was detected under the influence of cationic CTAB and nonionic TX-100 micelles. The change in the ionization pattern by micelles at pH values with biopharmaceutical significance provides indications of possible interactions of cetirizine with biomolecules of different charge and polarity under physiological conditions. Full article
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18 pages, 3468 KiB  
Review
Environmental Fate, Ecotoxicity, and Remediation of Heterocyclic Pharmaceuticals as Emerging Contaminants: A Review of Long-Term Risks and Impacts
by Oussama Baaloudj, Laura Scrano, Sabino Aurelio Bufo, Lee-Ann Sade Modley, Filomena Lelario, Angelica Rebecca Zizzamia, Lucia Emanuele and Monica Brienza
Organics 2025, 6(1), 1; https://doi.org/10.3390/org6010001 - 2 Jan 2025
Cited by 1 | Viewed by 1596
Abstract
Heterocyclic pharmaceuticals are emerging contaminants due to their toxic, carcinogenic nature and detrimental impact on the natural ecosystem. These compounds pose a significant environmental concern given their widespread use in medical therapy, constituting over 90% of new medications. Their unique chemical structure contributes [...] Read more.
Heterocyclic pharmaceuticals are emerging contaminants due to their toxic, carcinogenic nature and detrimental impact on the natural ecosystem. These compounds pose a significant environmental concern given their widespread use in medical therapy, constituting over 90% of new medications. Their unique chemical structure contributes to their persistence in various environmental matrices, necessitating urgent measures to mitigate their risks. This review comprehensively examines the sources, environmental fate, toxicity, and long-term risks associated with heterocyclic pharmaceuticals, proposing potential remediation strategies. The article commences with an overview of the diverse types of heterocyclic pharmaceuticals and their applications, focusing on compounds containing heteroatoms such as nitrogen, oxygen, and sulfur. Subsequently, it explores the sources and pathways through which these pollutants enter the environment, including wastewater discharge, agricultural runoff, improper disposal, resistance to biodegradation, and bioaccumulation. The toxic effects and long-term consequences of exposure to heterocyclic pharmaceuticals are then discussed, encompassing neurotoxicity, genotoxicity, mutagenesis, cardiovascular and metabolic toxicity, carcinogenicity, and teratogenesis. Additionally, this review summarizes various remediation strategies and treatment solutions aimed at reducing the environmental impact of these compounds, drawing insights from the literature. The research concludes by identifying critical areas for future research, emphasizing the urgent need for more effective remediation strategies to address the growing concern posed by these emerging contaminants. Full article
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