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From Electronic Structure to Application: Computational Insights into Bioactive and Functional Molecules

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 15 January 2026 | Viewed by 1451

Special Issue Editor


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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
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Special Issue Information

Dear Colleagues,

The search for new compounds with biological potential and the study of existing structures as drug candidates have become some of the most important tasks in modern chemistry. Currently, the fastest screening methods for evaluating the biological potential of molecules are techniques based on computational chemistry. Among these, the most popular and widely used include rule-based filtering, virtual high-throughput screening, similarity searching, molecular docking, and quantitative structure–activity relationships (QSAR).

With ongoing technological advancements, the use of in silico methods offers high predictive power. The results obtained help narrow down the scope of laboratory testing, which is often more time-consuming and requires specialized chemicals. Moreover, a thorough study of chemical compounds and an understanding of their electronic structure provide valuable insights not only for the medical industry but also for agrochemicals, electronics, and materials engineering.

Therefore, this Special Issue will focus on research concerning the structural properties of molecules based on reactivity descriptors, as well as their potential applications as biological agents and functional materials in various industries. In particular, we invite researchers to submit research and review articles on recent advances in this area.

Dr. Karolina Kula
Guest Editor

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Keywords

  • molecular design
  • molecular modeling
  • substituent effect
  • reactivity descriptors
  • biological potential
  • in silico study
  • physicochemical properties
  • ADME
  • PASS
  • QSAR

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Published Papers (2 papers)

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Research

38 pages, 6255 KB  
Article
In Silico Study About Substituent Effects, Electronic Properties, and the Biological Potential of 1,3-Butadiene Analogues
by Karolina Kula and Emilia Kuś
Int. J. Mol. Sci. 2025, 26(18), 8983; https://doi.org/10.3390/ijms26188983 - 15 Sep 2025
Viewed by 722
Abstract
1,3-Butadiene and its analogues constitute an important raw material in the petrochemical industry. What is more, due to their specific structure, these compounds are attractive components in the synthesis of heterocyclic compounds. Modification of the 1,3-butadiene structure allows obtaining compounds characterized by different [...] Read more.
1,3-Butadiene and its analogues constitute an important raw material in the petrochemical industry. What is more, due to their specific structure, these compounds are attractive components in the synthesis of heterocyclic compounds. Modification of the 1,3-butadiene structure allows obtaining compounds characterized by different reactivity and possessing various biological properties. In order to thoroughly investigate this phenomenon, an analysis of 20 compounds, including 1,3-butadiene and its analogues, was carried out. For this purpose, a study based on MEDT, ADME, and PASS was performed. In this research, changes in electronic properties and basic physicochemical parameters under the presence of various substituents at various positions in the structure of 1,3-butadiene were studied. At the end, the influence of modifications on biological activities for the tested compounds was evaluated. Based on the presented results, it was found that substituent modifications cause significant changes in both electronic structures and in physicochemical properties of all the compounds. This fact is probably caused by the small size of the considered compounds. On the other hand, the main preferences for the most important active sites in the tested molecules remain the same due to the presence of a strongly conjugated system of double bonds. Full article
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20 pages, 3358 KB  
Article
On the Question of the Regio-Orientation, Stereo-Orientation and Molecular Mechanism in the Cascade Cycloaddition/Rearrangement/Elimination Processes Leading to Nitro-Substituted Thiopyran Analogs: DFT Computational Study
by Mikołaj Sadowski, Ewa Dresler and Radomir Jasiński
Int. J. Mol. Sci. 2025, 26(18), 8948; https://doi.org/10.3390/ijms26188948 - 14 Sep 2025
Viewed by 540
Abstract
Sulfur-containing heterocyclic structures play an important role in modern biotechnology. Their synthesis is made possible by means of the hetero Diels–Alder reaction involving unsaturated sulfur compounds. In the framework of this paper, the molecular mechanism of the cycloaddition reactions between tioanalogs of the [...] Read more.
Sulfur-containing heterocyclic structures play an important role in modern biotechnology. Their synthesis is made possible by means of the hetero Diels–Alder reaction involving unsaturated sulfur compounds. In the framework of this paper, the molecular mechanism of the cycloaddition reactions between tioanalogs of the butadiene generated in situ with the participation of the Lawesson reagent and the E-2-phenyl-1-nitroethene was evaluated on the basis of the DFT quantum chemical calculations. It was found that the most favored reaction path is realized according to a stepwise mechanism with the participation of the zwitterionic intermediate. To study this further, the molecular mechanism of the deamination process of the primary cycloadducts was also analyzed. It was found that this mechanism is substantially different to the case of other known β-elimination processes and is achieved via a stepwise scheme. In addition to these investigations, the LA catalysis of the deamination process was also explored. Full article
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