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Exclusive Feature Papers on Molecular Structure

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

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 6926

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”. 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 physical chemistry 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.

Published Papers (7 papers)

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Research

10 pages, 1209 KiB  
Communication
Modeling Peptide–Protein Interactions by a Logo-Based Method: Application in Peptide–HLA Binding Predictions
by Irini Doytchinova, Mariyana Atanasova, Antonio Fernandez, F. Javier Moreno, Frits Koning and Ivan Dimitrov
Molecules 2024, 29(2), 284; https://doi.org/10.3390/molecules29020284 - 05 Jan 2024
Viewed by 747
Abstract
Peptide–protein interactions form a cornerstone in molecular biology, governing cellular signaling, structure, and enzymatic activities in living organisms. Improving computational models and experimental techniques to describe and predict these interactions remains an ongoing area of research. Here, we present a computational method for [...] Read more.
Peptide–protein interactions form a cornerstone in molecular biology, governing cellular signaling, structure, and enzymatic activities in living organisms. Improving computational models and experimental techniques to describe and predict these interactions remains an ongoing area of research. Here, we present a computational method for peptide–protein interactions’ description and prediction based on leveraged amino acid frequencies within specific binding cores. Utilizing normalized frequencies, we construct quantitative matrices (QMs), termed ‘logo models’ derived from sequence logos. The method was developed to predict peptide binding to HLA-DQ2.5 and HLA-DQ8.1 proteins associated with susceptibility to celiac disease. The models were validated by more than 17,000 peptides demonstrating their efficacy in discriminating between binding and non-binding peptides. The logo method could be applied to diverse peptide–protein interactions, offering a versatile tool for predictive analysis in molecular binding studies. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)
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11 pages, 1796 KiB  
Article
Synthesis, Structure, and Characterizations of a Volatile/Soluble Heterometallic Hexanuclear Precursor [NaMn2(thd)4(OAc)]2
by Yuxuan Zhang, Zheng Wei and Evgeny V. Dikarev
Molecules 2023, 28(23), 7795; https://doi.org/10.3390/molecules28237795 - 27 Nov 2023
Viewed by 560
Abstract
The paper describes a heterobimetallic mixed-ligand hexanuclear precursor [NaMn2(thd)4(OAc)]2 (1) (thd = 2,2,6,6-tetramethyl-3,5-heptadionate; OAc = acetate) that was designed based on its lithium homoleptic analogue, [LiMn2(thd)5], by replacing one of [...] Read more.
The paper describes a heterobimetallic mixed-ligand hexanuclear precursor [NaMn2(thd)4(OAc)]2 (1) (thd = 2,2,6,6-tetramethyl-3,5-heptadionate; OAc = acetate) that was designed based on its lithium homoleptic analogue, [LiMn2(thd)5], by replacing one of the thd ligands with an acetate group in order to accommodate 5-coordinated sodium instead of tetrahedral lithium ion. The complex, which is highly volatile and soluble in a variety of common solvents, has been synthesized by both the solid-state and solution methods. The unique “dimer-of-trimers” heterometallic structure consists of two trinuclear [NaMnII2(thd)4]+ units firmly bridged by two acetate ligands. X-ray diffraction techniques, DART mass spectrometry, ICP-OES analysis, and IR spectroscopy have been employed to confirm the structure and composition of the hexanuclear complex. Similar to the Li counterpart forming LiMn2O4 spinel material upon thermal decomposition, the title Na:Mn = 1:2 compound was utilized as the first single-source precursor for the low-temperature preparation of Na4Mn9O18 tunnel oxide. Importantly, four Mn sites in the hexanuclear molecule can be potentially partially substituted by other transition metals, leading to heterotri- and tetrametallic precursors for the advanced quaternary and quinary Na-ion oxide cathode materials. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)
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Graphical abstract

19 pages, 3156 KiB  
Article
NMR “Finger Prints” of N-Heterocyclic Carbenes, DFT Analysis: Scopes and Limitations
by Svetlana A. Kondrashova and Shamil K. Latypov
Molecules 2023, 28(23), 7729; https://doi.org/10.3390/molecules28237729 - 23 Nov 2023
Cited by 1 | Viewed by 626
Abstract
The scopes and limitations of theoretical methods for estimating various NMR metrics of NHCs are considered on a wide range of model NHCs and their derivatives, using a number of computational approximations. On the whole, the most reliable, from the point of view [...] Read more.
The scopes and limitations of theoretical methods for estimating various NMR metrics of NHCs are considered on a wide range of model NHCs and their derivatives, using a number of computational approximations. On the whole, the most reliable, from the point of view of predictability and insusceptibility to additional effects, are 31P/13C NMR shifts of NHC–phosphinidene adducts and 13C CSs of carbenes themselves. The method based on the analysis of 77Se CS NHC–selenoureas has some limitations since the observed NMR parameters can also be modulated by exchange effects due to their formation with non-classical hydrogen bonds. As for HEP, since the delicate balance of electron distribution between Pd and two carbon centers can nonlinearly affect relativistic spin–orbit effects, the accuracy of the estimation of this metric may still be limited. 13C CSs of NHC–azolium salts do not seem to be reliable, since the observed values are strongly influenced by the effects of the exchange between different forms with counterions, which are difficult to estimate correctly. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)
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Graphical abstract

8 pages, 3369 KiB  
Communication
Directional Crystallization of Conjugated Molecules during Coating Processes
by Detlef-M. Smilgies and Ruipeng Li
Molecules 2023, 28(14), 5371; https://doi.org/10.3390/molecules28145371 - 13 Jul 2023
Viewed by 613
Abstract
The coating of organic molecules from the solution phase can result in directional crystal growth under certain conditions, even on a smooth isotropic surface and without the need of any kind of graphoexpitaxial preparation of the substrate. Based on reviewing the results from [...] Read more.
The coating of organic molecules from the solution phase can result in directional crystal growth under certain conditions, even on a smooth isotropic surface and without the need of any kind of graphoexpitaxial preparation of the substrate. Based on reviewing the results from a variety of coating techniques and coating parameters, we identified that it is crucial for the coating speed to match the growth speed of the fastest growing crystal plane to achieve a high degree of directional crystallization. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)
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17 pages, 2505 KiB  
Article
Silver Ion High-Performance Liquid Chromatography—Atmospheric Pressure Chemical Ionization Mass Spectrometry: A Tool for Analyzing Cuticular Hydrocarbons
by Vladimír Vrkoslav, Petra Horká, Jindřich Jindřich, Miloš Buděšínský and Josef Cvačka
Molecules 2023, 28(9), 3794; https://doi.org/10.3390/molecules28093794 - 28 Apr 2023
Cited by 1 | Viewed by 1541
Abstract
Aliphatic hydrocarbons (HCs) are usually analyzed by gas chromatography (GC) or matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. However, analyzing long-chain HCs by GC is difficult because of their low volatility and the risk of decomposition at high temperatures. MALDI cannot distinguish between isomeric [...] Read more.
Aliphatic hydrocarbons (HCs) are usually analyzed by gas chromatography (GC) or matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. However, analyzing long-chain HCs by GC is difficult because of their low volatility and the risk of decomposition at high temperatures. MALDI cannot distinguish between isomeric HCs. An alternative approach based on silver ion high-performance liquid chromatography (Ag-HPLC) is shown here. The separation of HC standards and cuticular HCs was accomplished using two ChromSpher Lipids columns connected in series. A gradient elution of the analytes was optimized using mobile phases prepared from hexane (or isooctane) and acetonitrile, 2-propanol, or toluene. HCs were detected by atmospheric pressure chemical ionization mass spectrometry (APCI-MS). Good separation of the analytes according to the number of double bonds, cis/trans geometry, and position of double bonds was achieved. The retention times increased with the number of double bonds, and trans isomers eluted ahead of cis isomers. The mobile phase significantly affected the mass spectra of HCs. Depending on the mobile phase composition, deprotonated molecules, molecular ions, protonated molecules, and various solvent-related adducts of HCs were observed. The optimized Ag-HPLC/APCI-MS was applied for characterizing cuticular HCs from a flesh fly, Neobellieria bullata, and cockroach, Periplaneta americana. The method made it possible to detect a significantly higher number of HCs than previously reported for GC or MALDI-MS. Unsaturated HCs were frequently detected as isomers differing by double-bond position(s). Minor HCs with trans double bonds were found beside the prevailing cis isomers. Ag-HPLC/APCI-MS has great potential to become a new tool in chemical ecology for studying cuticular HCs. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)
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13 pages, 1506 KiB  
Article
Size–Pore-Dependent Methanol Sequestration from Water–Methanol Mixtures by an Embedded Graphene Slit
by Roger Bellido-Peralta, Fabio Leoni, Carles Calero and Giancarlo Franzese
Molecules 2023, 28(9), 3697; https://doi.org/10.3390/molecules28093697 - 25 Apr 2023
Cited by 1 | Viewed by 983
Abstract
The separation of liquid mixture components is relevant to many applications—ranging from water purification to biofuel production—and is a growing concern related to the UN Sustainable Development Goals (SDGs), such as “Clean water and Sanitation” and “Affordable and clean energy”. One promising technique [...] Read more.
The separation of liquid mixture components is relevant to many applications—ranging from water purification to biofuel production—and is a growing concern related to the UN Sustainable Development Goals (SDGs), such as “Clean water and Sanitation” and “Affordable and clean energy”. One promising technique is using graphene slit-pores as filters, or sponges, because the confinement potentially affects the properties of the mixture components in different ways, favoring their separation. However, no systematic study has shown how the size of a pore changes the thermodynamics of the surrounding mixture. Here, we focus on water–methanol mixtures and explore, using Molecular Dynamics simulations, the effects of a graphene pore, with size ranging from 6.5 to 13 Å, for three compositions: pure water, 90%–10%, and 75%–25% water–methanol. We show that tuning the pore size can change the mixture pressure, density and composition in bulk due to the size-dependent methanol sequestration within the pore. Our results can help in optimizing the graphene pore size for filtering applications. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)
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11 pages, 4496 KiB  
Article
Inclusion Complexes of 3,4-Ethylenedioxythiophene with Per-Modified β- and γ-Cyclodextrins
by Aurica Farcas, Ana-Maria Resmerita, Mihaela Balan-Porcarasu, Corneliu Cojocaru, Cristian Peptu and Ion Sava
Molecules 2023, 28(8), 3404; https://doi.org/10.3390/molecules28083404 - 12 Apr 2023
Cited by 4 | Viewed by 1179
Abstract
Herein, we report the synthesis of inclusion complexes (ICs) based on 3,4-ethylenedioxythiophene (EDOT) with permethylated β-cyclodextrins (TMe-βCD) and permethylated γ-cyclodextrins (TMe-γCD) host molecules. To prove the synthesis of such ICs, molecular docking simulation, UV-vis titrations in water, 1H-NMR, and H-H ROESY, as [...] Read more.
Herein, we report the synthesis of inclusion complexes (ICs) based on 3,4-ethylenedioxythiophene (EDOT) with permethylated β-cyclodextrins (TMe-βCD) and permethylated γ-cyclodextrins (TMe-γCD) host molecules. To prove the synthesis of such ICs, molecular docking simulation, UV-vis titrations in water, 1H-NMR, and H-H ROESY, as well as matrix-assisted laser desorption ionization mass spectroscopy (MALDI TOF MS) and thermogravimetric analysis (TGA) were carried out on each of the EDOT∙TMe-βCD and EDOT∙TMe-γCD samples. The results of computational investigations reveal the occurrence of hydrophobic interactions, which contribute to the insertion of the EDOT guest inside the macrocyclic cavities and a better binding of the neutral EDOT to TMe-βCD. The H-H ROESY spectra show correlation peaks between H-3 and H-5 of hosts and the protons of the guest EDOT, suggesting that the EDOT molecule is included inside the cavities. The MALDI TOF MS analysis of the EDOT∙TMe-βCD solutions clearly reveals the presence of MS peaks corresponding to sodium adducts of the species associated with the complex formation. The IC preparation shows remarkable improvements in the physical properties of EDOT, rendering it a plausible alternative to increasing its aqueous solubility and thermal stability. Full article
(This article belongs to the Special Issue Exclusive Feature Papers on Molecular Structure)
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