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Exclusive Feature Papers on Molecular Structure, 2nd Edition
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Exclusive Feature Papers on Molecular Structure, 2nd Edition

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

Deadline for manuscript submissions: 31 August 2025 | Viewed by 1624

Special Issue Editor

Prof. Dr. Chan Kyung Kim

E-Mail Website
Guest Editor
Department of Chemistry and Chemical Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
Interests: computational chemistry; high-energy density material design; computer-aided materials; drug design
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to announce the new Special Issue entitled “Exclusive Feature Papers on Molecular Structure, 2nd Edition”. This is a collection of important high-quality papers (original research articles or comprehensive reviews) published in open access format by Editorial Board Members or prominent scholars invited by the Editorial Office and the Guest Editors. We aim to gather state-of-the-art or new cutting-edge developments that cover all kinds of topics in the molecular structure field through selected works, in the hope of making a great contribution to the community. We intend for this Special Issue to serve as a forum for disseminating excellent research findings, as well as sharing innovative ideas in the field.

Prof. Dr. Chan Kyung Kim
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

  • molecular structure
  • chemical bonding
  • molecular clusters
  • molecular similarity
  • protein structure prediction
  • quantum chemistry
  • spectroscopy
  • molecular dynamics simulations

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Related Special Issue

Published Papers (3 papers)

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Research

13 pages, 2546 KiB  
Article
Interference Structures in the High-Order Above-Threshold Ionization Spectra of Polyatomic Molecules in a Bicircular Laser Field
by Elvedin Hasović, Azra Gazibegović-Busuladžić and Mustafa Busuladžić
Molecules 2025, 30(14), 2946; https://doi.org/10.3390/molecules30142946 - 11 Jul 2025
Viewed by 250
Abstract
We analyze the high-order above-threshold ionization (HATI) process of a small polyatomic molecule with C3 symmetry, which is induced by a bicircular strong laser field. This field consists of two coplanar, counter-rotating, circularly polarized components with frequencies rω and sω [...] Read more.
We analyze the high-order above-threshold ionization (HATI) process of a small polyatomic molecule with C3 symmetry, which is induced by a bicircular strong laser field. This field consists of two coplanar, counter-rotating, circularly polarized components with frequencies rω and sω where r and s are integers. In our study, we use an improved molecular strong-field approximation to obtain electron energy-angle-resolved and momentum spectra of the BF3 molecule. We analyze the contributions of individual atoms as well as the impact of molecular symmetries on these spectra. We find that these spectra are significantly affected by the characteristics of the molecule and the laser-field parameters. Furthermore, we observe pronounced interference minima in the HATI spectra. We demonstrate that these minima result from the destructive interference of rescattered wave packets from different atomic centers, and we determine the conditions under which they occur, including two-, three-, and four-center interference. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure, 2nd Edition)
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20 pages, 2721 KiB  
Article
Alpha and Omega Classification of β-Lactamase/Transpeptidase-like Superfamily Proteins Based on the Comparison of Their Structural Catalytic Cores
by Alexander I. Denesyuk, Konstantin Denessiouk, Mark S. Johnson and Vladimir N. Uversky
Molecules 2025, 30(9), 2019; https://doi.org/10.3390/molecules30092019 - 30 Apr 2025
Viewed by 521
Abstract
β-Lactamase/transpeptidase-like superfamily proteins are serine proteases that use the Ser–Lys catalytic dyad to carry out their biological functions. Here, we investigate the three known families of β-lactamase/transpeptidase-like superfamily proteins, β-lactamase/D-Ala carboxypeptidase, glutaminase, and Dac-like, and describe the structural catalytic cores that govern the [...] Read more.
β-Lactamase/transpeptidase-like superfamily proteins are serine proteases that use the Ser–Lys catalytic dyad to carry out their biological functions. Here, we investigate the three known families of β-lactamase/transpeptidase-like superfamily proteins, β-lactamase/D-Ala carboxypeptidase, glutaminase, and Dac-like, and describe the structural catalytic cores that govern the catalytic residues in these proteins. We show that the structural catalytic core of these proteins is a combination of three zones, the mutual three-dimensional arrangement of which correspondingly determines their belonging to one of seven and twenty-four established groups and subgroups. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure, 2nd Edition)
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24 pages, 5601 KiB  
Article
Binding Zinc and Oxo-Vanadium Insulin-Mimetic Complexes to Phosphatase Enzymes: Structure, Electronics and Implications
by Victor V. Volkov, Carole C. Perry and Riccardo Chelli
Molecules 2025, 30(7), 1469; https://doi.org/10.3390/molecules30071469 - 26 Mar 2025
Viewed by 610
Abstract
We explore the structural and electronic properties of representative insulin-mimetic oxovanadium and zinc complexes as computed in vacuum, in water clusters and upon binding to PTEN and PTP1B phosphatases. Albeit diverse, the enzymes’ active sites represent evolutionary variant choices of the same type [...] Read more.
We explore the structural and electronic properties of representative insulin-mimetic oxovanadium and zinc complexes as computed in vacuum, in water clusters and upon binding to PTEN and PTP1B phosphatases. Albeit diverse, the enzymes’ active sites represent evolutionary variant choices of the same type of biochemistry. Though different in respect to covalency and the orbital nature of bonding, theory predicts comparable ionic radii, bond lengths and square pyramidal coordination for the considered vanadyl and zinc systems when in an aqueous environment. Employing docking, DFT and quantum mechanics/molecular mechanics methods, we address possible polar interactions in the protein environments and compute infrared/Raman modes and optical electronic properties, which may be suitable for the structural analysis of the specific chemical moieties in binding studies. Accounting for how protein embedding may alter the electronic states of metal centres, we discuss artificial intelligence-assisted protein field engineering to assist biomedical and quantum information applications. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure, 2nd Edition)
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