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Quantum Chemical Calculations of Molecular Reaction Processes, 2nd Edition
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Quantum Chemical Calculations of Molecular Reaction Processes, 2nd Edition

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

Deadline for manuscript submissions: 30 November 2025 | Viewed by 1219

Special Issue Editors

Dr. Naoki Kishimoto

E-Mail Website
Guest Editor
Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
Interests: computational chemistry; quantum chemical calculations
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Shiro Koseki

E-Mail Website
Guest Editor
Department of Chemistry, Graduate School of Science, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
Interests: computational chemistry; quantum chemical calculations
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Theoretical chemical calculations are becoming increasingly important in molecular science and are indispensable for elucidating complex chemical reaction processes and quantitatively predicting observations. The accuracy of quantum chemical calculations has been supported by developments in electronic state theory and the increasing speed of computers. In quantum chemical calculations for reactions, novel algorithms have been developed to reveal reaction pathways, and eventually artificial intelligence will be used to a great extent for molecular design.

In this Special Issue, we will feature papers that use quantum chemical calculations to reveal the reaction processes of molecules. As an open access journal, we will make the potential of quantum chemical calculations widely known to the world by publishing the latest results on using computers to understand the complex world of chemistry.

Dr. Naoki Kishimoto
Prof. Dr. Shiro Koseki
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • computational chemistry
  • electronic structure
  • MO theory
  • DFT calculation
  • reaction process
  • Ab initio molecular dynamics
  • molecular design

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Related Special Issue

Published Papers (3 papers)

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Research

16 pages, 4479 KiB  
Article
Photophysical Properties of 1,3-Diphenylisobenzofuran as a Sensitizer and Its Reaction with O2
by Ștefan Stan, João P. Prates Ramalho, Alexandru Holca and Vasile Chiș
Molecules 2025, 30(14), 3021; https://doi.org/10.3390/molecules30143021 - 18 Jul 2025
Viewed by 328
Abstract
1,3-Diphenylisobenzofuran (DPBF) is a widely used fluorescent probe for singlet oxygen (1O2) detection in photodynamic applications. In this work, we present an integrated experimental and computational analysis to describe its spectroscopic, photophysical, and reactive properties in ethanol, DMSO, and [...] Read more.
1,3-Diphenylisobenzofuran (DPBF) is a widely used fluorescent probe for singlet oxygen (1O2) detection in photodynamic applications. In this work, we present an integrated experimental and computational analysis to describe its spectroscopic, photophysical, and reactive properties in ethanol, DMSO, and DMF. UV-Vis and fluorescence measurements across a wide concentration range show well-resolved S0 → S1 electronic transition of a π → π* nature with small red shifts in polar aprotic solvents. Fluorescence lifetimes increase slightly with solvent polarity, showing stabilization of the excited state. The 2D PES and Boltzmann populations analysis indicate two co-existing conformers (Cs and C2), with Cs being slightly more stable at room temperature. TD-DFT calculations have been performed using several density functionals and the 6-311+G(2d,p) basis set to calculate absorption/emission wavelengths, oscillator strengths, transition dipole moments, and radiative lifetimes. Overall, cam-B3LYP and ωB97X-D provided the best agreement with experiments for the photophysical data across all solvents. The photophysical behavior of DPBF upon interaction with 1O2 can be explained by a small-barrier, two-step reaction pathway that goes through a zwitterionic intermediate, resulting in the formation of 2,5-endoperoxide. This work explains the photophysical properties and reactivity of DPBF, therefore providing a solid basis for future studies involving singlet oxygen. Full article
(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes, 2nd Edition)
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11 pages, 1085 KiB  
Article
In Search of New Drugs: Elucidating the Activity of Structurally Similar Potential Antibiotics Using Molecular Modelling
by Natalina Makieieva, Teobald Kupka, Piotr Lodowski, Radosław Balwierz, Katarzyna Kasperkiewicz, Adam Byrski, Roksolana Konechna and Vira Lubenets
Molecules 2025, 30(14), 2920; https://doi.org/10.3390/molecules30142920 - 10 Jul 2025
Viewed by 282
Abstract
The global problem of antibiotic resistance leads to the necessity for drug improvement and discovery. Natural and synthetic sulfur-containing compounds have been known as antibiotics for many years. In the current study, we demonstrated an antibacterial activity of three new thiosulfonates: S-ethyl 4-aminobenzene-1-sulfonothioate [...] Read more.
The global problem of antibiotic resistance leads to the necessity for drug improvement and discovery. Natural and synthetic sulfur-containing compounds have been known as antibiotics for many years. In the current study, we demonstrated an antibacterial activity of three new thiosulfonates: S-ethyl 4-aminobenzene-1-sulfonothioate (1), S-methyl 4-acetamidobenzene-1-sulfonothioate (2), and S-ethyl 4-acetamidobenzene-1-sulfonothioate (3). Their activities were studied on two model Gram-positive and Gram-negative bacteria strains: Staphylococcus aureus ATTC 6538P and Escherichia coli ATTC 8739, respectively. According to the literature data, we proposed a general mechanism of 1−3 biochemical actions. To analyze its feasibility, theoretical studies using density functional theory (DFT) were performed. The obtained results demonstrate a direct correlation between some NBO parameters and the S-S bond energy of 1−3 with their activity against both studied bacterial strains. The obtained results could be helpful for future biomedical studies on the analyzed compounds and promote the further design of new S-containing antibiotics. Full article
(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes, 2nd Edition)
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14 pages, 2707 KiB  
Article
Understanding Bio-Orthogonal Strain-Driven Sydnone Cycloadditions: Data-Assisted Profiles and the Search for Linear Relationships
by Juan García de la Concepción, Pedro Cintas and Rafael Fernando Martínez
Molecules 2025, 30(13), 2770; https://doi.org/10.3390/molecules30132770 - 27 Jun 2025
Viewed by 345
Abstract
In the realm of click-type reactions and their application to bioorthogonal chemistry in living organisms, metal-free [3+2] cycloadditions involving mesoionic rings and strained cycloalkynes have gained increasing attention and potentiality in recent years. While there has been a significant accretion of experimental data, [...] Read more.
In the realm of click-type reactions and their application to bioorthogonal chemistry in living organisms, metal-free [3+2] cycloadditions involving mesoionic rings and strained cycloalkynes have gained increasing attention and potentiality in recent years. While there has been a significant accretion of experimental data, biological assays, and assessments of reaction mechanisms, some pieces of the tale are still missing. For instance, which structural and/or stereoelectronic effects are actually interlocked and which remain unplugged. With the advent of data-driven methods, including machine learning simulations, quantitative estimations of relevant observables and their correlations will explore better the chemical space of these transformations. Here we unveil a series of linear relationships, such as Hammett-type correlations, as well as deviations of linearity, using the case study of phenylsydnone (and its 4-aryl-substituted derivatives) with a highly reactive bicyclo[6.1.0]nonyne carbinol. Through accurate estimation of activation barriers and prediction of rate constants, our findings further increase the significance of integrating strain release and electronic effects in organic reactivity. Moreover, such results could pave the way to use mesoionics cycloadditions as probes for measuring the extent of delocalization-assisted strain release, which can be applied to related reactions involving dipoles and strained rings. Full article
(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes, 2nd Edition)
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