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Selected Papers Associated with the Modeling and Design of Molecular Materials (MDMM 2022) Conference

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 15827

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Special Issue Editors

Prof. Dr. Janusz Rak

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Guest Editor

Department of Chemistry, University of Gdańsk, 80-233 Gdańsk, Poland
Interests: DNA damage; radiation chemistry; photochemistry; quantum-chemistry
Special Issues, Collections and Topics in MDPI journals

Dr. Lidia Chomicz-Mańka

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Guest Editor

Laboratory of Biological Sensitizers, Department of Physical Chemistry, Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
Interests: radiosensitizers; density functional theory; quantum chemical calculations; low-energy electrons; dissociative electron attachment; DNA damage; oxygen mimetics; modified nucleosides
Special Issues, Collections and Topics in MDPI journals

Dr. Magdalena Zdrowowicz

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Guest Editor

Department of Chemistry, University of Gdańsk, 80-233 Gdańsk, Poland
Interests: radiosensitizers; photosensitizers; DNA damage; radiobiology; cellular studies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Modeling and Design of Molecular Materials 2022 (MDMM 2022) conference is an interdisciplinary meeting devoted to the various aspects of conceiving materials with predefined properties. The key term is “molecular material”, which in the context of the conference means drugs and drug carriers (focused on cancer), catalysts, with an emphasis on photocatalysis (e.g., solar energy conversion) or theozymes (theoretically designed biocatalysts), materials for hydrogen storage (green fuel), conductive polymers (e.g., electronics, biosensors), etc. Nowadays, computer modeling seems to be a crucial step for the rational design of materials with demanded properties. Thus, during this prospective event we hope to gather specialists who develop computational methods useful in the computer-aided design of materials as well as those who employ molecular modeling at the very early stages of their projects and for whom a computational approach eventually leads to practical solutions. Besides papers related directly to the presentations delivered during the conference, we warmly invite all those researchers whose work employs computational models for designing materials which can be used in medicine (drugs and drug carriers), catalysis, solar energy conversion, hydrogen storage, biosensors, etc.

For submissions from the MDMM 2022 conference, the publication partner IJMS agrees to grant a special discount of 20%.

Prof. Dr. Janusz Rak
Dr. Lidia Chomicz-Mańka
Dr. Magdalena Zdrowowicz
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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 chemistry
molecular dynamics
chemometrics
small-molecule drugs
drug carriers
photocatalysts and catalysts
theozymes
hydrogen storage materials
conductive polymers

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Published Papers (7 papers)

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Research

14 pages, 464 KiB

Open AccessArticle

Artificial Intelligence in Decrypting Cytoprotective Activity under Oxidative Stress from Molecular Structure

by Damian Nowak, Karolina Babijczuk, La Ode Irman Jaya, Rafał Adam Bachorz, Lucyna Mrówczyńska, Beata Jasiewicz and Marcin Hoffmann

Int. J. Mol. Sci. 2023, 24(14), 11349; https://doi.org/10.3390/ijms241411349 - 12 Jul 2023

Cited by 1 | Viewed by 1736

Abstract

Artificial intelligence (AI) is widely explored nowadays, and it gives opportunities to enhance classical approaches in QSAR studies. The aim of this study was to investigate the cytoprotective activity parameter under oxidative stress conditions for indole-based structures, with the ultimate goal of developing AI models capable of predicting cytoprotective activity and generating novel indole-based compounds. We propose a new AI system capable of suggesting new chemical structures based on some known cytoprotective activity. Cytoprotective activity prediction models, employing algorithms such as random forest, decision tree, support vector machines, K-nearest neighbors, and multiple linear regression, were built, and the best (based on quality measurements) was used to make predictions. Finally, the experimental evaluation of the computational results was undertaken in vitro. The proposed methodology resulted in the creation of a library of new indole-based compounds with assigned cytoprotective activity. The other outcome of this study was the development of a validated predictive model capable of estimating cytoprotective activity to a certain extent using molecular structure as input, supported by experimental confirmation. Full article

(This article belongs to the Special Issue Selected Papers Associated with the Modeling and Design of Molecular Materials (MDMM 2022) Conference)

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14 pages, 2043 KiB

Open AccessArticle

Electron-Induced Decomposition of 5-Bromo-4-thiouracil and 5-Bromo-4-thio-2′-deoxyuridine: The Effect of the Deoxyribose Moiety on Dissociative Electron Attachment

by Farhad Izadi, Adrian Szczyrba, Magdalena Datta, Olga Ciupak, Sebastian Demkowicz, Janusz Rak and Stephan Denifl

Int. J. Mol. Sci. 2023, 24(10), 8706; https://doi.org/10.3390/ijms24108706 - 13 May 2023

Cited by 3 | Viewed by 1628

Abstract

When modified uridine derivatives are incorporated into DNA, radical species may form that cause DNA damage. This category of molecules has been proposed as radiosensitizers and is currently being researched. Here, we study electron attachment to 5-bromo-4-thiouracil (BrSU), a uracil derivative, and 5-bromo-4-thio-2′-deoxyuridine (BrSdU), with an attached deoxyribose moiety via the N-glycosidic (N1-C) bond. Quadrupole mass spectrometry was used to detect the anionic products of dissociative electron attachment (DEA), and the experimental results were supported by quantum chemical calculations performed at the M062X/aug-cc-pVTZ level of theory. Experimentally, we found that BrSU predominantly captures low-energy electrons with kinetic energies near 0 eV, though the abundance of bromine anions was rather low compared to a similar experiment with bromouracil. We suggest that, for this reaction channel, proton-transfer reactions in the transient negative ions limit the release of bromine anions. Full article

(This article belongs to the Special Issue Selected Papers Associated with the Modeling and Design of Molecular Materials (MDMM 2022) Conference)

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13 pages, 3412 KiB

Open AccessArticle

Mechanism of Silylation of Vinyl Arenes by Hydrodisiloxanes Driven by Stoichiometric Amounts of Sodium Triethylborohydride—A Combined DFT and Experimental Study

by Mateusz Nowicki, Maciej Zaranek, Magdalena Grzelak, Piotr Pawluć and Marcin Hoffmann

Int. J. Mol. Sci. 2023, 24(5), 4924; https://doi.org/10.3390/ijms24054924 - 3 Mar 2023

Viewed by 1692

Abstract

The reactions of vinyl arenes with hydrodisiloxanes in the presence of sodium triethylborohydride were studied using experimental and computational methods. The expected hydrosilylation products were not detected because triethylborohydrides did not exhibit the catalytic activity observed in previous studies; instead, the product of formal silylation with dimethylsilane was identified, and triethylborohydride was consumed in stoichiometric amounts. In this article, the mechanism of the reaction is described in detail, with due consideration given to the conformational freedom of important intermediates and the two-dimensional curvature of the potential energy hypersurface cross sections. A simple way to reestablish the catalytic character of the transformation was identified and explained with reference to its mechanism. The reaction presented here is an example of the application of a simple transition-metal-free catalyst in the synthesis of silylation products, with flammable gaseous reagents replaced by a more convenient silane surrogate. Full article

(This article belongs to the Special Issue Selected Papers Associated with the Modeling and Design of Molecular Materials (MDMM 2022) Conference)

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12 pages, 5332 KiB

Open AccessArticle

Change in the Nature of ZSM-5 Zeolite Depending on the Type of Metal Adsorbent—The Analysis of DOS and Orbitals for Iron Species

by Izabela Kurzydym, Alberto Garbujo, Pierdomenico Biasi and Izabela Czekaj

Int. J. Mol. Sci. 2023, 24(4), 3374; https://doi.org/10.3390/ijms24043374 - 8 Feb 2023

Cited by 1 | Viewed by 1796

Abstract

Transition-metal-modified zeolites have recently gained the greatest interest among scientists. Ab initio calculations within the density functional theory were used. The exchange and correlation functional was approximated with the Perdew–Burke–Ernzerhof (PBE) functional. Cluster models of ZSM-5 (Al₂Si₁₈O₅₃H₂₆) zeolites were used with Fe particles adsorbed above aluminum. The adsorption of three iron adsorbates inside the pores of the ZSM-5 zeolite—Fe, FeO and FeOH—was carried out with different arrangements of aluminum atoms in the zeolite structure. The DOS diagram and the HOMO, SOMO and LUMO molecular orbitals for these systems were analyzed. It has been shown that depending on the adsorbate and the position of aluminum atoms in the pore structure of the zeolite, the systems can be described as insulators or conductors, which significantly affects their activity. The main aim of the research was to understand the behavior of these types of systems in order to select the most efficient one for a catalytic reaction. Full article

(This article belongs to the Special Issue Selected Papers Associated with the Modeling and Design of Molecular Materials (MDMM 2022) Conference)

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17 pages, 1248 KiB

Open AccessArticle

Neural Networks in the Design of Molecules with Affinity to Selected Protein Domains

by Damian Nowak, Rafał Adam Bachorz and Marcin Hoffmann

Int. J. Mol. Sci. 2023, 24(2), 1762; https://doi.org/10.3390/ijms24021762 - 16 Jan 2023

Cited by 5 | Viewed by 3545

Abstract

Drug design with machine learning support can speed up new drug discoveries. While current databases of known compounds are smaller in magnitude (approximately

10^{8}

), the number of small drug-like molecules is estimated to be between

10^{23}

and

10^{60}

. [...] Read more.

Drug design with machine learning support can speed up new drug discoveries. While current databases of known compounds are smaller in magnitude (approximately

10^{8}

), the number of small drug-like molecules is estimated to be between

10^{23}

and

10^{60}

. The use of molecular docking algorithms can help in new drug development by sieving out the worst drug-receptor complexes. New chemical spaces can be efficiently searched with the application of artificial intelligence. From that, new structures can be proposed. The research proposed aims to create new chemical structures supported by a deep neural network that will possess an affinity to the selected protein domains. Transferring chemical structures into SELFIES codes helped us pass chemical information to a neural network. On the basis of vectorized SELFIES, new chemical structures can be created. With the use of the created neural network, novel compounds that are chemically sensible can be generated. Newly created chemical structures are sieved by the quantitative estimation of the drug-likeness descriptor, Lipinski’s rule of 5, and the synthetic Bayesian accessibility classifier score. The affinity to selected protein domains was verified with the use of the AutoDock tool. As per the results, we obtained the structures that possess an affinity to the selected protein domains, namely PDB IDs 7NPC, 7NP5, and 7KXD. Full article

(This article belongs to the Special Issue Selected Papers Associated with the Modeling and Design of Molecular Materials (MDMM 2022) Conference)

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11 pages, 5262 KiB

Open AccessArticle

Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO₃]⁻: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints

by Qiaolin Wang, Zhengbo Qin, Gao-Lei Hou, Zheng Yang, Marat Valiev, Xue-Bin Wang, Xianfeng Zheng and Zhifeng Cui

Int. J. Mol. Sci. 2023, 24(2), 1682; https://doi.org/10.3390/ijms24021682 - 14 Jan 2023

Cited by 2 | Viewed by 2084

Abstract

L-cysteine S-sulfate, Cys-SSO₃H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO₃]⁻ was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO₃]^• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO₃]⁻ (S₁) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O−H⋯⋯N between the –COOH and –NH₂ groups, and two N−H⋯⋯O HBs between –NH₂ and –SO₃, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S₂) with the formation of an O−H⋯⋯N−H⋯⋯O−S chain-type binding motif competes with S₁ in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O−H and N−H stretching modes are the fingerprint region (2800 to 3600 cm⁻¹) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure–reactivity correlation of Cys-SSO₃H in biologic settings. Full article

(This article belongs to the Special Issue Selected Papers Associated with the Modeling and Design of Molecular Materials (MDMM 2022) Conference)

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27 pages, 7346 KiB

Open AccessArticle

Isopropyl Amino Acid Esters Ionic Liquids as Vehicles for Non-Steroidal Anti-Inflammatory Drugs in Potential Topical Drug Delivery Systems with Antimicrobial Activity

by Joanna Klebeko, Oliver Krüger, Mateusz Dubicki, Paula Ossowicz-Rupniewska and Ewa Janus

Int. J. Mol. Sci. 2022, 23(22), 13863; https://doi.org/10.3390/ijms232213863 - 10 Nov 2022

Cited by 8 | Viewed by 2000

Abstract

New derivatives of non-steroidal anti-inflammatory drugs were synthesized via conjugation with L-amino acid isopropyl esters. The characteristics of the physicochemical properties of the obtained pharmaceutically active ionic liquids were determined. It has been shown how the incorporation of various L-amino acid esters as an ion pair affects the properties of the parent drug. Moreover, the antimicrobial activity of the obtained compounds was evaluated. The proposed structural modifications of commonly used drugs indicate great potential for use in topical and transdermal preparations. Full article

(This article belongs to the Special Issue Selected Papers Associated with the Modeling and Design of Molecular Materials (MDMM 2022) Conference)

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