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30th Anniversary of Molecules—Recent Advances in Computational and Theoretical Chemistry

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 2026 | Viewed by 2483

Special Issue Editor

Dr. Maxim L. Kuznetsov

E-Mail Website
Guest Editor
Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Avenue Rovisco Pais, 1049-001 Lisbon, Portugal
Interests: computational chemistry; coordination chemistry; molecular catalysis; oxidation of hydrocarbons; activation of small molecules; reaction mechanism; chemical bond nature; non-covalent interactions; cycloaddition
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue celebrates the 30th anniversary of Molecules, one of the leading forums for the dissemination of high-quality research of broad interest in chemical science. Over the last three decades, Molecules has evolved from a pioneering open access journal in organic and natural product chemistry to a comprehensive platform encompassing all facets of chemistry. It currently plays a pivotal role in advancing our understanding of various chemical systems, fostering innovation across disciplines.

Theoretical and computational methods have emerged as indispensable pillars of modern chemistry, offering profound insights into molecular behavior and facilitating advancements across various domains, including but not restricted to drug discovery, material science, nanotechnology, and reaction mechanisms. These methods provide powerful tools to complement experimental studies, bridging the gap between theory and practice and pushing the boundaries of chemistry.

This Special Issue aims to gather high-quality contributions that reflect the profound impact of theoretical and computational methods in modern chemical science. We hope this it will demonstrate the latest developments in this field and highlight the critical role of computational and theoretical methods in shaping the future of chemistry.

Previously unpublished manuscripts in the field of theoretical and computational chemistry or those employing broadly theoretical or computational methods are welcome in this Special Issue.

Dr. Maxim L. Kuznetsov
Guest Editor

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
  • quantum chemistry
  • density functional theory
  • molecular design
  • reaction mechanism
  • chemical bonding
  • non-covalent interactions
  • molecular docking

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Published Papers (5 papers)

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Research

18 pages, 1830 KiB  
Article
Discovery of Novel Inhibitors of Aspergillus fumigatus DHODH via Virtual Screening, MD Simulation, and In Vitro Activity Assay
by Kaige Li, Wei Xia and John Z. H. Zhang
Molecules 2025, 30(12), 2607; https://doi.org/10.3390/molecules30122607 - 16 Jun 2025
Viewed by 248
Abstract
To address the surge in Aspergillus fumigatus infections among immunosuppressed patients and azole resistance, this study focused on developing novel inhibitors targeting dihydroorotate dehydrogenase (AfDHODH), a key enzyme in fungal pyrimidine synthesis. The three-dimensional structure of AfDHODH was constructed via homology modeling. Molecular [...] Read more.
To address the surge in Aspergillus fumigatus infections among immunosuppressed patients and azole resistance, this study focused on developing novel inhibitors targeting dihydroorotate dehydrogenase (AfDHODH), a key enzyme in fungal pyrimidine synthesis. The three-dimensional structure of AfDHODH was constructed via homology modeling. Molecular docking, dynamics simulations, and binding free energy calculations systematically elucidated the mechanisms of existing inhibitors. Virtual screening against the ZINC20 and ChEMBL databases yielded 13 candidates, with two micromolar inhibitors (IC50 < 100 μM) identified through in vitro assays. These inhibitors exhibited novel scaffold structures that were distinct from known DHODH inhibitors. The results validate the feasibility of homology modeling-guided antifungal discovery and these findings provide critical insights for the development of new antifungal agents. Full article
(This article belongs to the Special Issue 30th Anniversary of Molecules—Recent Advances in Computational and Theoretical Chemistry)
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24 pages, 3364 KiB  
Article
One-Pot Approach Towards Peptoids Synthesis Using 1,4-Dithiane-2,5-Diol via Multicomponent Approach and DFT-Based Computational Analysis
by Musrat Shaheen and Akbar Ali
Molecules 2025, 30(11), 2340; https://doi.org/10.3390/molecules30112340 - 27 May 2025
Viewed by 595
Abstract
Peptoids are peptidomimetics in which the side chain is attached to the nitrogen of the amide group rather than the α-carbon. This alteration in the backbone structure is highly valued because it endows beneficial properties, including enhanced resistance to proteolysis, greater immunogenicity, [...] Read more.
Peptoids are peptidomimetics in which the side chain is attached to the nitrogen of the amide group rather than the α-carbon. This alteration in the backbone structure is highly valued because it endows beneficial properties, including enhanced resistance to proteolysis, greater immunogenicity, improved biostability, and superior bioavailability. In this current study, we focused on the Ugi-4CR-based one-pot synthesis of peptoids using 1,4-dithiane-2,5-diol as the carbonyl component together with amine, carboxylic acid, and isocyanides. Four new peptoids—5a, 5b, 5c, and 5d—were designed and efficiently prepared in good chemical yields and were subjected to DFT investigations for their electronic behavior. These compounds have free OH, SH, and terminal triple bonds for further chemistry. In a computational analysis, the spectral data of compounds 5a–5d were juxtaposed with calculated spectral values derived from the B3LYP/6-311G(d,p) level. The electronic excitation and orbital contributions of 5a–5d were predicted using TD-DFT calculations. A natural bond order (NBO) analysis was utilized to investigate the electronic transition of newly synthesized peptoids, focusing on their charge distribution patterns. Furthermore, MEP and NPA analyses were conducted to predict charge distribution in these compounds. The reactivity and stability of the targeted peptoids were evaluated by global reactivity descriptors, which were determined with frontier molecular orbital analysis. The DFT results revealed that compound 5c displayed marginally higher reactivity compared to 5a, 5b, and 5d, possibly due to its extended conjugation. Full article
(This article belongs to the Special Issue 30th Anniversary of Molecules—Recent Advances in Computational and Theoretical Chemistry)
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17 pages, 6900 KiB  
Article
Tuning the Energy Levels of Adamantane by Boron Substitution
by Aminu H. Yusuf, Vladimir B. Golovko and Sarah L. Masters
Molecules 2025, 30(9), 1976; https://doi.org/10.3390/molecules30091976 - 29 Apr 2025
Viewed by 483
Abstract
Adamantane is known to have two different carbon environments, the C1-type (or bridgehead) and C2-type (or methylene bridge), serving as a foundation to explore the effects of boron substitution at these sites. Using DFT with B3LYP/6-31G(d), the structural, electronic, and optical properties of [...] Read more.
Adamantane is known to have two different carbon environments, the C1-type (or bridgehead) and C2-type (or methylene bridge), serving as a foundation to explore the effects of boron substitution at these sites. Using DFT with B3LYP/6-31G(d), the structural, electronic, and optical properties of 37 boron-substituted isomers were investigated. The adamantane structure has rigid Td symmetry with an average rC-C of 153.7 pm, which progressively transforms to C3v and C1 symmetry in heavily substituted isomers. Analysis of the neutral and ionic species reveals a critical transition from electron-donating to electron-accepting behaviour at tri-boron substitution, confirmed by both DFT and coupled cluster calculations (CCSD(T)/CC-pVDZ). C1 substitution narrows the HOMO–LUMO gap significantly, achieving a 56% reduction compared to 44.5% for C2 substitution in tetra-bora derivatives compared to adamantane. Optical properties [CAM-B3LYP/6-311G(d,p)] show systematic red shifting with increasing boron substitution, with absorption maxima moving from 146 nm in pristine adamantane to 423 nm (C1) and 277 nm (C2) in heavily boron-substituted derivatives (tetra-bora-adamantane). While C1 substitution leads to symmetry-forbidden transitions, C2 substitution maintains allowed transitions, offering more consistent optical behaviour. These findings provide important insight for the design of adamantane-based materials with tailored electronic and optical properties. Full article
(This article belongs to the Special Issue 30th Anniversary of Molecules—Recent Advances in Computational and Theoretical Chemistry)
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11 pages, 1982 KiB  
Article
Hydroperoxyl Radical Scavenging Activity of Bromophenols from Marine Red Alga Polysiphonia urceolata: Mechanistic Insights, Kinetic Analysis, and Influence of Physiological Media
by Houssem Boulebd
Molecules 2025, 30(8), 1697; https://doi.org/10.3390/molecules30081697 - 10 Apr 2025
Viewed by 339
Abstract
Bromophenols (BPs), particularly those derived from marine sources, are known for their potent radical scavenging activity, effectively neutralizing reactive oxygen species (ROS). However, their exact mechanism of action remains largely unexplored, limiting our understanding of their potential as natural antioxidants. In this study, [...] Read more.
Bromophenols (BPs), particularly those derived from marine sources, are known for their potent radical scavenging activity, effectively neutralizing reactive oxygen species (ROS). However, their exact mechanism of action remains largely unexplored, limiting our understanding of their potential as natural antioxidants. In this study, the antiradical mechanisms of two BP derivatives (1 and 2), previously isolated from the marine red alga Polysiphonia urceolata, were systematically investigated using thermodynamic and kinetic calculations. Both compounds demonstrated potent hydroperoxyl radical (HOO•) scavenging activity in polar and lipid environments, with rate constants surpassing those of the well-known antioxidant standards Trolox and BHT. In lipid media, BP 2 exhibited approximately 600-fold greater activity than BP 1, with rate constants of 9.75 × 105 and 1.64 × 103 M−1 s−1, respectively. In contrast, both BPs showed comparable activity in aqueous media, with rate constants of 3.46 × 108 and 9.67 × 108 M−1 s−1 for 1 and 2, respectively. Mechanistic analysis revealed that formal hydrogen atom transfer (f-HAT) is the predominant pathway for radical scavenging in both lipid and polar environments. These findings provide critical insights into the antiradical mechanisms of natural BPs and underscore the potential of BP 1 and BP 2 as highly effective hydroperoxyl radical scavengers under physiological conditions. Full article
(This article belongs to the Special Issue 30th Anniversary of Molecules—Recent Advances in Computational and Theoretical Chemistry)
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19 pages, 5194 KiB  
Article
Structural, Electronic, and Nonlinear Optical Characteristics of Europium-Doped Germanium Anion Nanocluster EuGen− (n = 7–20): A Theoretical Investigation
by Chenliang Hao, Xueyan Dong, Chunli Li, Caixia Dong, Zhaofeng Yang and Jucai Yang
Molecules 2025, 30(6), 1377; https://doi.org/10.3390/molecules30061377 - 19 Mar 2025
Cited by 1 | Viewed by 512
Abstract
Doping rare-earth metals into semiconductor germanium clusters can significantly enhance the stability of these clusters while introducing novel and noteworthy optical properties. Herein, a series of EuGen− (n = 7–20) clusters and their structural and nonlinear optical properties are investigated [...] Read more.
Doping rare-earth metals into semiconductor germanium clusters can significantly enhance the stability of these clusters while introducing novel and noteworthy optical properties. Herein, a series of EuGen− (n = 7–20) clusters and their structural and nonlinear optical properties are investigated via the ABCluster global search technique combined with the double-hybrid density functional theory mPW2PLYP. The structure growth pattern can be divided into two stages: an adsorption structure and a linked structure (when n = 7–10 and n = 11–20, respectively). In addition to simulating the photoelectron spectra of the clusters, their various properties, including their (hyper)polarizability, magnetism, charge transfer, relative stability, and energy gap, are identified. According to our examination, the EuGe13− cluster exhibits a significant nonlinear optical response of the βtot value of 7.47 × 105 a.u., and is thus considered a promising candidate for outstanding nonlinear optical semiconductor nanomaterials. Full article
(This article belongs to the Special Issue 30th Anniversary of Molecules—Recent Advances in Computational and Theoretical Chemistry)
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