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Heterocyclic Compounds: Synthesis, Application and Theoretical Study
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Heterocyclic Compounds: Synthesis, Application and Theoretical Study

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Organic Chemistry".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 12425

Special Issue Editor

Dr. Karolina Kula

E-Mail Website
Guest Editor
Department of Organic Chemistry and Technology, Cracow University of Technology, Warszawska 24, 31-155 Krakow, Poland
Interests: organic synthesis; cycloaddition reaction; regio- and stereoselectivity; heterocycle chemistry; chromatography; spectroscopy; quantum–chemical calculation; density functional theory (DFT); molecular electron density theory (MEDT); nitroalkene; nitrodiene
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The effective design and sustainable synthesis of novel heterocyclic compounds are the main focus points in modern chemistry. The constant interest of scientists in this class of organic compounds is caused by their unique properties. Heterocycles are important not only for the pharmacy industry but also for the agrochemical and dyeing industries. Therefore, this Special Issue will cover the most recent trends in the chemistry of heterocyclic compounds. In particular, we invite researchers to publish their recent short laboratory notes and full papers on the synthesis of these compounds (including structural studies), their properties, biological activities, and potential applications. We also welcome theoretical considerations based on the analysis of electron densities applied to synthetic aspects, reaction mechanisms, and structural analyses. The submissions of review articles written by experts in this field will also be appreciated.

Dr. Karolina Kula
Guest Editor

Manuscript Submission Information

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Keywords

  • synthesis and transformation of heterocycles
  • structural chemistry
  • reaction mechanisms
  • stereochemistry
  • regiochemistry
  • quantum chemical computations
  • biological activity of heterocyclic compounds
  • green chemistry

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Published Papers (7 papers)

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Research

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15 pages, 1112 KB  
Article
Synthesis of New Brassinosteroid Analogs with Androstane Skeleton and Heterocyclic Acyl Side Chains: Preliminary Molecular Docking Studies
by Omara Araya, María Núñez, Marco Mellado, Andrés F. Olea and Luis Espinoza-Catalán
Molecules 2025, 30(19), 4011; https://doi.org/10.3390/molecules30194011 - 7 Oct 2025
Viewed by 409
Abstract
Brassinosteroid analogs with heterocyclic rings in the side chain are interesting because important biological activity has been shown by these compounds. Thus, herein, five 23-24-dinorcholane BR analogs with a heterocyclic ester function at C-22 were synthesized and fully characterized by different spectroscopic techniques. [...] Read more.
Brassinosteroid analogs with heterocyclic rings in the side chain are interesting because important biological activity has been shown by these compounds. Thus, herein, five 23-24-dinorcholane BR analogs with a heterocyclic ester function at C-22 were synthesized and fully characterized by different spectroscopic techniques. The acylation reaction at C-22, which is a key synthetic step, was carried out by two different methods, namely acylation with heterocyclic acid chlorides and Steglich esterification reaction. In both cases, the acyl derivatives were obtained with good yields. Additionally, a preliminary molecular docking study of BRI1–BAK1 complexes formed by these analogs and brassinolide was performed to estimate what their biological activity would be. Results indicate that the complex formed by the analog 36, which has an indole group in the side chain, within the active site of BRI1–BAK1 is more stable than that formed by brassinolide. Additionally, molecular docking of a derivative having a benzoate function at C-22 and a F atom in the ortho position, 23, shows a similar pose and interactions at the active site but the highest binding energy. As 23 has shown similar activity to brassinolide in the Rice Lamina Inclination Test, it is expected that 36 will also exhibit similar behavior. Full article
(This article belongs to the Special Issue Heterocyclic Compounds: Synthesis, Application and Theoretical Study)
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19 pages, 7596 KB  
Article
A Novel Method of Coupling In Situ Time-Resolved FTIR and Microwave Irradiation: Application to the Monitoring of Quinoxaline Derivatives Synthesis
by Alina Cherniienko, Kacper Kossakowski, Lucjusz Zaprutko, Roman Lesyk, Dorota Olender and Anna Pawełczyk
Molecules 2025, 30(19), 3875; https://doi.org/10.3390/molecules30193875 - 25 Sep 2025
Viewed by 435
Abstract
Traditional synthetic methods, often limited by inefficiency, are increasingly being replaced by sustainable alternatives. This study presents a green approach combining microwave irradiation with in situ FTIR spectroscopy for real-time monitoring and optimising nitrogen-heterocycle synthesis, focusing on quinoxalines. Although both microwave-assisted synthesis and [...] Read more.
Traditional synthetic methods, often limited by inefficiency, are increasingly being replaced by sustainable alternatives. This study presents a green approach combining microwave irradiation with in situ FTIR spectroscopy for real-time monitoring and optimising nitrogen-heterocycle synthesis, focusing on quinoxalines. Although both microwave-assisted synthesis and time-resolved FTIR are established techniques, their combined application remains underexplored, limiting their synergistic potential. The methodology was applied to synthesising 2,3-diphenylquinoxaline, a compound of interest in medicinal chemistry. Optimisation of the condensation between benzil and 1,2-phenylenediamine was achieved by exploiting the accelerated kinetics of microwave irradiation and continuous monitoring via in situ FTIR. Three catalytic systems were evaluated—hydrochloric acid (Brønsted acid), Montmorillonite K10 (heterogeneous catalyst), and molecular iodine (halogen/Lewis acid)—alongside a range of solvents, including ethanol, methanol, water, acetonitrile, ethyl acetate, dimethyl sulfoxide, and dichloromethane. Iodine proved to be the most efficient catalyst, while acetonitrile and ethyl acetate provided the most effective solvent systems. This integrated monitoring strategy reduces reliance on trial-and-error optimisation and establishes a streamlined, scalable, and efficient protocol. The dual-technique approach highlights a versatile pathway for advancing green synthetic methodologies with applications across the chemical and pharmaceutical industries. Full article
(This article belongs to the Special Issue Heterocyclic Compounds: Synthesis, Application and Theoretical Study)
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20 pages, 2552 KB  
Article
A Remarkable Selectivity Observed in Hetero-Diels–Alder Reactions of Levoglucosenone (LGO) with Thiochalcones: An Experimental and Computational Study
by Grzegorz Mlostoń, Katarzyna Urbaniak, Marcin Palusiak, Ernst-Ulrich Würthwein, Hans-Ulrich Reissig and Zbigniew J. Witczak
Molecules 2025, 30(18), 3783; https://doi.org/10.3390/molecules30183783 - 17 Sep 2025
Viewed by 469
Abstract
Levoglucosenone (LGO) smoothly undergoes microwave-assisted hetero-Diels–Alder reactions with thiochalcones in THF solution at 60 °C. The studied reactions are completed after 10 min, and the expected tricyclic 2,3-dihydro-4H-thiopyran derivatives are formed in a highly regio- and moderately stereoselective manner via competitive [...] Read more.
Levoglucosenone (LGO) smoothly undergoes microwave-assisted hetero-Diels–Alder reactions with thiochalcones in THF solution at 60 °C. The studied reactions are completed after 10 min, and the expected tricyclic 2,3-dihydro-4H-thiopyran derivatives are formed in a highly regio- and moderately stereoselective manner via competitive exo- and endo-attacks of the 1-thiadiene moiety onto the activated C=C bond of dienophile LGO. Although eight isomers are possible, only the formation of exo,exo- (major) and exo,endo- (minor) cycloadducts was observed. In most cases, isomeric products were separated by preparative layer chromatography and identified by means of spectroscopic methods. Some of the cycloadducts were obtained as single crystalline solids, and X-ray analyses enabled unambiguous confirmation of their structures. In order to explain the observed selectivity of the studied hetero-Diels–Alder reactions, DFT studies were carried out to determine the thermodynamic and kinetic properties of all regio- and stereoisomers. The results of these calculations predict the preferred formation of the two experimentally observed isomers. In addition, remarkable details on the electronic structure of E-1,3-diphenylprop-2-en-1-thione and on involved and hypothetical transition states could be elucidated. Full article
(This article belongs to the Special Issue Heterocyclic Compounds: Synthesis, Application and Theoretical Study)
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18 pages, 3234 KB  
Article
Mechanistic Aspects of [3+2] Cycloaddition Reaction of Trifluoroacetonitrile with Diarylnitrilimines in Light of Molecular Electron Density Theory Quantum Chemical Study
by Agnieszka Łapczuk and Mar Ríos-Gutiérrez
Molecules 2025, 30(1), 85; https://doi.org/10.3390/molecules30010085 - 29 Dec 2024
Cited by 4 | Viewed by 1840
Abstract
In this study, we investigated the [3+2] cycloaddition reaction of CF3CN (TFAN) with nitrilimine (NI) to produce 1,2,4-triazole and compared the resulting isomers. We determined the preferred reaction pathway by examining the electrophilic and nucleophilic properties of the reaction substrates, performing [...] Read more.
In this study, we investigated the [3+2] cycloaddition reaction of CF3CN (TFAN) with nitrilimine (NI) to produce 1,2,4-triazole and compared the resulting isomers. We determined the preferred reaction pathway by examining the electrophilic and nucleophilic properties of the reaction substrates, performing thermodynamic calculations for the individual pathways, and comparing them with the experimental results. Full article
(This article belongs to the Special Issue Heterocyclic Compounds: Synthesis, Application and Theoretical Study)
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24 pages, 6486 KB  
Article
Unexpected Course of Reaction Between (1E,3E)-1,4-Dinitro-1,3-butadiene and N-Methyl Azomethine Ylide—A Comprehensive Experimental and Quantum-Chemical Study
by Mikołaj Sadowski and Karolina Kula
Molecules 2024, 29(21), 5066; https://doi.org/10.3390/molecules29215066 - 26 Oct 2024
Cited by 27 | Viewed by 2367
Abstract
In recent times, interest in the chemistry of conjugated nitrodienes is still significantly increasing. In particular, the application of these compounds as building blocks to obtain heterocycles is a popular object of research. Therefore, in continuation of our research devoted to the topic [...] Read more.
In recent times, interest in the chemistry of conjugated nitrodienes is still significantly increasing. In particular, the application of these compounds as building blocks to obtain heterocycles is a popular object of research. Therefore, in continuation of our research devoted to the topic of conjugated nitrodienes, experimental and quantum-chemical studies of a cycloaddition reaction between (1E,3E)-1,4-dinitro-1,3-butadiene and N-methyl azomethine ylide have been investigated. The computational results present that the tested reaction is realized through a pdr-type polar mechanism. In turn, the experimental study shows that in a course of this cycloaddition, only one reaction product in the form of 1-methyl-3-(trans-2-nitrovinyl)-Δ3-pyrroline is created. The constitution of this compound has been confirmed via spectroscopic methods. Finally, ADME analysis indicated that the synthesized Δ3-pyrroline exhibits biological potential, and it is a good drug candidate according to Lipinski, Veber and Egan rules. Nevertheless, PASS simulation showed that the compound exhibits weak antimicrobial, inhibitory and antagonist properties. Preliminary in silico research shows that although the obtained Δ3-pyrroline is not a good candidate for a drug, the presence of a nitrovinyl moiety in its structure indicates that the compound is an initial basis for further modifications. Full article
(This article belongs to the Special Issue Heterocyclic Compounds: Synthesis, Application and Theoretical Study)
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20 pages, 5554 KB  
Article
Syn-Propanethial S-Oxide as an Available Natural Building Block for the Preparation of Nitro-Functionalized, Sulfur-Containing Five-Membered Heterocycles: An MEDT Study
by Mikołaj Sadowski, Ewa Dresler, Karolina Zawadzińska, Aneta Wróblewska and Radomir Jasiński
Molecules 2024, 29(20), 4892; https://doi.org/10.3390/molecules29204892 - 15 Oct 2024
Cited by 18 | Viewed by 2682
Abstract
The regio- and stereoselectivity and the molecular mechanisms of the [3 + 2] cycloaddition reactions between Syn-propanethial S-oxide and selected conjugated nitroalkenes were explored theoretically in the framework of the Molecular Electron Density Theory. It was found that cycloadditions with the participation [...] Read more.
The regio- and stereoselectivity and the molecular mechanisms of the [3 + 2] cycloaddition reactions between Syn-propanethial S-oxide and selected conjugated nitroalkenes were explored theoretically in the framework of the Molecular Electron Density Theory. It was found that cycloadditions with the participation of nitroethene as well as its methyl- and chloro-substituted analogs can be realized via a single-step mechanism. On the other hand, [3 + 2] cycloaddition reactions between Syn-propanethial S-oxide and 1,1-dinitroethene can proceed according to a stepwise mechanism with a zwitterionic intermediate. Finally, we evaluated the affinity of model reaction products for several target proteins: cytochrome P450 14α-sterol demethylase CYP51 (RSCB Database PDB ID: 1EA1), metalloproteinase gelatinase B (MMP-9; PDB ID: 4XCT), and the inhibitors of cyclooxygenase COX-1 (PDB:3KK6) and COX-2 (PDB:5KIR). Full article
(This article belongs to the Special Issue Heterocyclic Compounds: Synthesis, Application and Theoretical Study)
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Review

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26 pages, 7686 KB  
Review
Recent Advances in Visible Light-Induced C-H Functionalization of Imidazo[1,2-a]pyridines
by Juanjuan Gao, Xinlei Fu, Kai Yang and Zhaowen Liu
Molecules 2025, 30(3), 607; https://doi.org/10.3390/molecules30030607 - 30 Jan 2025
Cited by 2 | Viewed by 3225
Abstract
The imidazo[1,2-a]pyridine skeleton is widely present in many natural products and pharmaceutical agents. Due to its impressive and significant biological activities, such as analgesic, anti-tumor, antiosteoporosis, and anxiolytic properties, the derivatization of imidazo[1,2-a]pyridine skeleton has attracted widespread attention from chemists. In recent years, [...] Read more.
The imidazo[1,2-a]pyridine skeleton is widely present in many natural products and pharmaceutical agents. Due to its impressive and significant biological activities, such as analgesic, anti-tumor, antiosteoporosis, and anxiolytic properties, the derivatization of imidazo[1,2-a]pyridine skeleton has attracted widespread attention from chemists. In recent years, significant progress has been made in the derivatization of imidazo[1,2-a]pyridines through direct C-H functionalization, especially through visible light induction. This review highlights recent advances in visible light-induced C-H functionalization of imidazo[1,2-a]pyridines during the past ten years, and some reaction mechanisms are also discussed. Full article
(This article belongs to the Special Issue Heterocyclic Compounds: Synthesis, Application and Theoretical Study)
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