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Molecular Modeling: Advancements and Applications, 3rd 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 June 2025 | Viewed by 5571

Special Issue Editor

Special Issue Information

Dear Colleagues,

It is generally accepted that quantum mechanics, theoretical chemistry, and theoretical physics are all very hermetic branches of science. However, their more recent incarnations, such as computational chemistry and molecular modeling, are also widely used in the laboratory by more practically oriented scientists. This is mainly due to the enormous progress we have witnessed, since the middle of the 20th century, in theoretical developments and even more so in computer hardware and software. The first milestone in computational chemistry and molecular modeling developments can be traced back to the theoretical prediction of the hydrogen molecule’s dissociation energy by Włodzimierz Kołos and Lutosław Wolniewicz in 1960, surpassing the most accurate experimental values determined earlier by Gerhard Herzberg and his team. Later on, in 1998, John Pople was awarded the Nobel Prize for his development of computational methods in quantum chemistry together with Walter Kohn, one of the fathers of the density functional theory. In the few most recent decades, both in basic and applied sciences, we have witnessed an avalanche of new methods and applications of molecular modeling in chemistry, pharmacy, and material sciences.

Molecular modeling has been used mainly for the following two reasons:

  1. Structure and property prediction of new molecular systems.
  2. Support for the analysis of experimental data, including UV–VIS, IR/Raman, and NMR spectra.

Presently, the quest for novel methodologies is challenged by drug design and material sciences. One of the important factors in this race is software development. Among the important factors of molecular modeling developments is the demand for accuracy, achieved mainly for small molecular systems. With the increasing size and complexity of the systems under investigation, they are often treated at a lower level of theoretical sophistication. In both cases, the speed of computer calculation and the available storage size are the limiting factors.

The aim of this Special Issue is to provide potential readers with an overview of recent challenges and developments in the fields of computational chemistry and molecular modeling, particularly those pertaining to various spectroscopic methods employed by experimental chemists and scientists working in pharmacy and the material sciences.

Reviews, full papers, and short communications covering the methodology, theory, and application aspects of molecular modeling are equally welcomed. The submission of papers addressing the topics listed below is particularly encouraged.

Prof. Dr. Teobald Kupka
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

  • quantum mechanics
  • molecular mechanics (MM)
  • molecular dynamics (MD)
  • semi-empirical calculations
  • Ab initio methods
  • post-Hartree–Fock methods
  • density functional theory (DFT)
  • software development
  • achieving chemical accuracy
  • thermochemistry and reactivity
  • interaction energy
  • covalent bonding and non-covalent interactions
  • large molecular systems
  • IR, Raman, and NMR
  • drug design
  • nanomaterials and nanotechnology
  • material sciences

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Published Papers (5 papers)

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Research

15 pages, 6194 KiB  
Article
Towards Imaging Tau Hyperphosphorylation: Is DYRK1A a Potential Target for Imaging Hyperphosphorylation of Tau? Molecular Modeling Assessment and Synthesis of [125I]Radioiodinated DYRK1A Inhibitor
by Cayz G. Paclibar, Deanna M. Schafer, Agnes P. Biju, Fariha Karim, Stephanie A. Sison, Christopher Liang, Shamiha T. Ahmed and Jogeshwar Mukherjee
Molecules 2025, 30(5), 990; https://doi.org/10.3390/molecules30050990 - 21 Feb 2025
Viewed by 564
Abstract
Dual specificity tyrosine-phosphorylation regulated kinase 1A (DYRK1A), a phosphorylation kinase, is localized within the central nervous system and is linked to hyperphosphorylation of Tau. Imaging of DYRK1A may provide an earlier biomarker for Tauopathies, including Alzheimer’s disease (AD). We have used Chimera-Autodock to [...] Read more.
Dual specificity tyrosine-phosphorylation regulated kinase 1A (DYRK1A), a phosphorylation kinase, is localized within the central nervous system and is linked to hyperphosphorylation of Tau. Imaging of DYRK1A may provide an earlier biomarker for Tauopathies, including Alzheimer’s disease (AD). We have used Chimera-Autodock to evaluate potential molecules for binding to the binding site of DYRK1A. Five molecules, 10-bromo-2-iodo-11H-indolo[3,2-c]quinoline-6-carboxylic acid (4E3), 10-iodo-11H-indolo[3,2-c]quinoline-6-carboxylic acid (KuFal184), harmine, 6-(fluoro-3-(1H-pyrrolo[2,3-c]pyridin-1-yl)isoquinolin-5-amine (MK-6240), and 6-iodo-3-(1H-pyrrolo[2,3-c]pyridine-1-yl)isoquinoline (IPPI), were found to have binding energies of −10.4, −10.1, −9.0, −9.1, and −9.4 kcal/mole, respectively. Two molecules, 4E3 and KuFal184, were selective for DYRK1A, while harmine also had a monoamine oxidase A affinity, and MK-6240 and IPPI had affinity for Tau. Tau present in the brain slices of AD subject were labeled with [125I]IPPI. KuFal184 had no effect on the binding of [125I]IPPI, suggesting the absence of binding overlap of the two molecules. MK-6240, a known Tau agent was, however, able to compete with [125I]IPPI. The binding energies of harmine, MK-6240, and IPPI for the DYRK1A site suggest affinities of approximately 80–100 nM, which is insufficient to serve as an imaging agent. The higher affinity of KuFal184 (6 nM for DYRK1A) suggested that [125I]KuFal184 may be a potential imaging agent. Electrophilic radioiodination was used to synthesize [125I]KuFal184 in modest yields (25%) and high radiochemical purity (>95%). Preliminary binding studies with [125I]KuFal184 in AD brain slices showed some selectivity for cortical grey matter regions containing Tau. Full article
(This article belongs to the Special Issue Molecular Modeling: Advancements and Applications, 3rd Edition)
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8 pages, 1214 KiB  
Article
Variation in (Hyper)Polarizability of H2 Molecule in Bond Dissociation Processes Under Spatial Confinement
by Paweł Lipkowski and Wojciech Bartkowiak
Molecules 2025, 30(1), 9; https://doi.org/10.3390/molecules30010009 - 24 Dec 2024
Viewed by 550
Abstract
We report the results of calculations of the linear polarizability and second hyperpolarizability of the H2 molecule in the bond dissociation process. These calculations were performed for isolated molecules, as well as molecules under spatial confinement. The spatial confinement was modeled using [...] Read more.
We report the results of calculations of the linear polarizability and second hyperpolarizability of the H2 molecule in the bond dissociation process. These calculations were performed for isolated molecules, as well as molecules under spatial confinement. The spatial confinement was modeled using the external two-dimensional (cylindrical) harmonic oscillator potential. In contrast to the recently investigated polar LiH molecule, it was shown that the spatial confinement significantly diminishes the linear and nonlinear response of H2 for each interatomic (H-H) distance. Full article
(This article belongs to the Special Issue Molecular Modeling: Advancements and Applications, 3rd Edition)
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11 pages, 3913 KiB  
Article
Molecular Docking of Endolysins for Studying Peptidoglycan Binding Mechanism
by Arina G. Arakelian, Gennady N. Chuev and Timur V. Mamedov
Molecules 2024, 29(22), 5386; https://doi.org/10.3390/molecules29225386 - 15 Nov 2024
Viewed by 1422
Abstract
Endolysins of bacteriophages, which degrade the bacterial cell wall peptidoglycan, are applicable in many industries to deal with biofilms and bacterial infections. While multi-domain endolysins have both enzymatically active and cell wall-binding domains, single-domain endolysins consist only of an enzymatically active domain, and [...] Read more.
Endolysins of bacteriophages, which degrade the bacterial cell wall peptidoglycan, are applicable in many industries to deal with biofilms and bacterial infections. While multi-domain endolysins have both enzymatically active and cell wall-binding domains, single-domain endolysins consist only of an enzymatically active domain, and their mechanism of peptidoglycan binding remains unexplored, for this is a challenging task experimentally. This research aimed to explore the binding mechanism of endolysins using computational approaches, namely molecular docking and bioinformatical tools, and analyze the performance of these approaches. The docking engine Autodock Vina 1.1.2 and the 3D-RISM module of AmberTools 24 were studied in the current work and used for receptor–ligand affinity and binding energy calculations, respectively. Two possible mechanisms of single-domain endolysin–ligand binding were predicted by Autodock Vina and verified by the 3D-RISM. As a result, the previously obtained experimental results on peptidoglycan binding of the isolated gamma phage endolysin PlyG enzymatically active domain were supported by molecular docking. Both methods predicted that single-domain endolysins are able to bind peptidoglycan, with Autodock Vina being able to give accurate numerical estimates of protein–ligand affinities and 3D-RISM providing comparative values. Full article
(This article belongs to the Special Issue Molecular Modeling: Advancements and Applications, 3rd Edition)
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10 pages, 3643 KiB  
Article
Mechanisms of Atomic Oxygen Erosion in Fluorinated Polyimides Investigated by Molecular Dynamics Simulations
by Shengrui Zhou, Li Zhang, Liang Zou, Bilal Iqbal Ayubi and Yiwei Wang
Molecules 2024, 29(18), 4485; https://doi.org/10.3390/molecules29184485 - 21 Sep 2024
Cited by 2 | Viewed by 979
Abstract
Traditional polyimides have highly conjugated structures, causing significant coloration under visible light. Fluorinated colorless polyimides, known for their light weight and excellent optical properties, are considered ideal for future aerospace optical lenses. However, their lifespan in low Earth orbit is severely limited by [...] Read more.
Traditional polyimides have highly conjugated structures, causing significant coloration under visible light. Fluorinated colorless polyimides, known for their light weight and excellent optical properties, are considered ideal for future aerospace optical lenses. However, their lifespan in low Earth orbit is severely limited by high-density atomic oxygen (AO) erosion, and the degradation behavior of fluorinated polyimides under AO exposure is not well understood. This study uses reactive molecular dynamics simulations to model two fluorinated polyimides, PMDA-TFMB and 6FDA-TFMB, with different fluorine contents, to explore their degradation mechanisms under varying AO concentrations. The results indicate that 6FDA-TFMB has slightly better resistance to erosion than PMDA-TFMB, mainly due to the enhanced chemical stability from its -CF3 groups. As AO concentration increases, widespread degradation of the polyimides occurs, with AO-induced cleavage and temperature-driven pyrolysis happening simultaneously, producing CO and OH as the main degradation products. This study uncovers the molecular-level degradation mechanisms of fluorinated polyimides, offering new insights for the design of AO erosion protection systems. Full article
(This article belongs to the Special Issue Molecular Modeling: Advancements and Applications, 3rd Edition)
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18 pages, 3728 KiB  
Article
Very Strong Hydrogen Bond in Nitrophthalic Cocrystals
by Kinga Jóźwiak, Aneta Jezierska, Jarosław J. Panek, Andrzej Kochel, Barbara Łydżba-Kopczyńska and Aleksander Filarowski
Molecules 2024, 29(15), 3565; https://doi.org/10.3390/molecules29153565 - 29 Jul 2024
Viewed by 1467
Abstract
This work presents the studies of a very strong hydrogen bond (VSHB) in biologically active phthalic acids. Research on VSHB comes topical due to its participation in many biological processes. The studies cover the modelling of intermolecular interactions and phthalic acids with 2,4,6-collidine [...] Read more.
This work presents the studies of a very strong hydrogen bond (VSHB) in biologically active phthalic acids. Research on VSHB comes topical due to its participation in many biological processes. The studies cover the modelling of intermolecular interactions and phthalic acids with 2,4,6-collidine and N,N-dimethyl-4-pyridinamine complexes with aim to obtain a VSHB. The four synthesized complexes were studied by experimental X-ray, IR, and Raman methods, as well as theoretical Car–Parrinello Molecular Dynamics (CP-MD) and Density Functional Theory (DFT) simulations. By variation of the steric repulsion and basicity of the complex’ components, a very short intramolecular hydrogen bond was achieved. The potential energy curves calculated by the DFT method were characterized by a low barrier (0.7 and 0.9 kcal/mol) on proton transfer in the OHN intermolecular hydrogen bond for 3-nitrophthalic acid with either 2,4,6-collidine or N,N-dimethyl-4-pyridinamine cocrystals. Moreover, the CP-MD simulations exposed very strong bridging proton dynamics in the intermolecular hydrogen bonds. The accomplished crystallographic and spectroscopic studies indicate that the OHO intramolecular hydrogen bond in 4-nitrophthalic cocrystals is VSHB. The influence of a strong steric effect on the geometry of the studied cocrystals and the stretching vibration bands of the carboxyl and carboxylate groups was elaborated. Full article
(This article belongs to the Special Issue Molecular Modeling: Advancements and Applications, 3rd Edition)
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