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Special Issue "Feature Papers in 'Physical Chemistry and Chemical Physics' 2023"

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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: 31 December 2023 | Viewed by 7282

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Prof. Dr. Dongho Kim

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Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
Interests: physical chemistry; time- and space-resolved spectroscopy; ground and excited state aromaticity; energy and electron transfer; molecular aggregation; molecular symmetry; exciton localization and delocalization dynamics; excimer dynamics
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Special Issue Information

Dear Colleagues,

This Special Issue entitled "Feature Papers in Physical Chemistry and Chemical Physics 2023" aims to collect high-quality original research articles, communications, and comprehensive review papers (4000+ words) in the cutting-edge field of physics and chemistry. We encourage the Editorial Board Members of the International Journal of Molecular Sciences to contribute feature papers reflecting the latest progress in their research field or to invite relevant experts and colleagues to do so.

Prof. Dr. Dongho Kim
Guest Editor

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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.

Published Papers (11 papers)

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Research

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Open AccessArticle

Impact of Non-Covalent Interactions of Chiral Linked Systems in Solution on Photoinduced Electron Transfer Efficiency

Alexander B. Doktorov

and

Tatyana V. Leshina

Int. J. Mol. Sci. 2023, 24(11), 9296; https://doi.org/10.3390/ijms24119296 - 26 May 2023

Viewed by 277

Abstract

It is well-known that non-covalent interactions play an essential role in the functioning of biomolecules in living organisms. The significant attention of researchers is focused on the mechanisms of associates formation and the role of the chiral configuration of proteins, peptides, and amino acids in the association. We have recently demonstrated the unique sensitivity of chemically induced dynamic nuclear polarization (CIDNP) formed in photoinduced electron transfer (PET) in chiral donor–acceptor dyads to non-covalent interactions of its diastereomers in solutions. The present study further develops the approach for quantitatively analyzing the factors that determine the association by examples of dimerization of the diastereomers with the RS, SR, and SS optical configurations. It has been shown that, under the UV irradiation of dyads, CIDNP is formed in associates, namely, homodimers (SS-SS), (SR-SR), and heterodimers (SS-SR) of diastereomers. In particular, the efficiency of PET in homo-, heterodimers, and monomers of dyads completely determines the forms of dependences of the CIDNP enhancement coefficient ratio of SS and RS, SR configurations on the ratio of diastereomer concentrations. We expect that the use of such a correlation can be useful in identifying small-sized associates in peptides, which is still a problem. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Open AccessArticle

Spin-Forbidden Addition of Molecular Oxygen to Stable Enol Intermediates—Decarboxylation of 2-Methyl-1-tetralone-2-carboxylic Acid

Pablo Ortega

Sara Gil-Guerrero

Lola González-Sánchez

Cristina Sanz-Sanz

and

Pablo G. Jambrina

Int. J. Mol. Sci. 2023, 24(8), 7424; https://doi.org/10.3390/ijms24087424 - 18 Apr 2023

Viewed by 473

Abstract

The deprotonation of an organic substrate is a common preactivation step for the enzymatic cofactorless addition of O

_{2}

to this substrate, as it promotes charge-transfer between the two partners, inducing intersystem crossing between the triplet and singlet states involved in the process. [...] Read more.

The deprotonation of an organic substrate is a common preactivation step for the enzymatic cofactorless addition of O

_{2}

to this substrate, as it promotes charge-transfer between the two partners, inducing intersystem crossing between the triplet and singlet states involved in the process. Nevertheless, the spin-forbidden addition of O

_{2}

to uncharged ligands has also been observed in the laboratory, and the detailed mechanism of how the system circumvents the spin-forbiddenness of the reaction is still unknown. One of these examples is the cofactorless peroxidation of 2-methyl-3,4-dihydro-1-naphthol, which will be studied computationally using single and multi-reference electronic structure calculations. Our results show that the preferred mechanism is that in which O

_{2}

picks a proton from the substrate in the triplet state, and subsequently hops to the singlet state in which the product is stable. For this reaction, the formation of the radical pair is associated with a higher barrier than that associated with the intersystem crossing, even though the absence of the negative charge leads to relatively small values of the spin-orbit coupling. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Open AccessArticle

High-Performance Potassium-Selective Biosensor Platform Based on Resistive Coupling of a-IGZO Coplanar-Gate Thin-Film Transistor

Tae-Hwan Hyun

and

Won-Ju Cho

Int. J. Mol. Sci. 2023, 24(7), 6164; https://doi.org/10.3390/ijms24076164 - 24 Mar 2023

Viewed by 650

Abstract

The potassium (K⁺) ion is an essential mineral for balancing body fluids and electrolytes in biological systems and regulating bodily function. It is associated with various disorders. Given that it exists at a low concentration in the human body and should be maintained at a precisely stable level, the development of highly efficient potassium-selective sensors is attracting considerable interest in the healthcare field. Herein, we developed a high-performance, potassium-selective field-effect transistor-type biosensor platform based on an amorphous indium gallium zinc oxide coplanar-gate thin-film transistor using a resistive coupling effect with an extended gate containing a potassium-selective membrane. The proposed sensor can detect potassium in KCl solutions with a high sensitivity of 51.9 mV/dec while showing a low sensitivity of <6.6 mV/dec for NaCl, CaCl₂, and pH buffer solutions, indicating its high selectivity to potassium. Self-amplification through the resistive-coupling effect enabled an even greater potassium sensitivity of 597.1 mV/dec. Additionally, we ensured the stability and reliability of short- and long-term detection through the assessment of non-ideal behaviors, including hysteresis and drift effects. Therefore, the proposed potassium-sensitive biosensor platform is applicable to high-performance detection in a living body, with high sensitivity and selectivity for potassium. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Open AccessArticle

Secondary and Topological Structural Merge Prediction of Alpha-Helical Transmembrane Proteins Using a Hybrid Model Based on Hidden Markov and Long Short-Term Memory Neural Networks

and

Int. J. Mol. Sci. 2023, 24(6), 5720; https://doi.org/10.3390/ijms24065720 - 16 Mar 2023

Viewed by 543

Abstract

Alpha-helical transmembrane proteins (αTMPs) play essential roles in drug targeting and disease treatments. Due to the challenges of using experimental methods to determine their structure, αTMPs have far fewer known structures than soluble proteins. The topology of transmembrane proteins (TMPs) can determine the spatial conformation relative to the membrane, while the secondary structure helps to identify their functional domain. They are highly correlated on αTMPs sequences, and achieving a merge prediction is instructive for further understanding the structure and function of αTMPs. In this study, we implemented a hybrid model combining Deep Learning Neural Networks (DNNs) with a Class Hidden Markov Model (CHMM), namely HDNNtopss. DNNs extract rich contextual features through stacked attention-enhanced Bidirectional Long Short-Term Memory (BiLSTM) networks and Convolutional Neural Networks (CNNs), and CHMM captures state-associative temporal features. The hybrid model not only reasonably considers the probability of the state path but also has a fitting and feature-extraction capability for deep learning, which enables flexible prediction and makes the resulting sequence more biologically meaningful. It outperforms current advanced merge-prediction methods with a Q4 of 0.779 and an MCC of 0.673 on the independent test dataset, which have practical, solid significance. In comparison to advanced prediction methods for topological and secondary structures, it achieves the highest topology prediction with a Q2 of 0.884, which has a strong comprehensive performance. At the same time, we implemented a joint training method, Co-HDNNtopss, and achieved a good performance to provide an important reference for similar hybrid-model training. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Open AccessArticle

A Comprehensive Ab Initio Study of Halogenated A···U and G···C Base Pair Geometries and Energies

Rosa M. Gomila

Antonio Frontera

and

Antonio Bauzá

Int. J. Mol. Sci. 2023, 24(6), 5530; https://doi.org/10.3390/ijms24065530 - 14 Mar 2023

Viewed by 504

Abstract

Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of “Atoms in Molecules” (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Open AccessArticle

Quantum-Chemical Prediction of Molecular and Electronic Structure of Carbon-Nitrogen Chemical Compound with Unusual Ratio Atoms: C(N₂₀)

Oleg V. Mikhailov

and

Denis V. Chachkov

Int. J. Mol. Sci. 2023, 24(6), 5172; https://doi.org/10.3390/ijms24065172 - 08 Mar 2023

Viewed by 494

Abstract

Using various versions of quantum-chemical calculation, namely four versions of density functional theory (DFT), (DFT B3PW91/TZVP, DFT M06/TZVP, DFT B3PW91/Def2TZVP, and DFT M06/Def2TZVP) and two versions of the MP method (MP2/TZVP and MP3/TZVP), the existence possibility of the carbon-nitrogen-containing compound having an unusual M: nitrogen ratio of 1:20, unknown for these elements at present, was shown. Structural parameters data are presented; it was noted that, as may be expected, CN₄ grouping has practically a tetrahedral structure, and the chemical bond lengths formed by nitrogen atoms and a carbon atom in the frameworks of each of the calculation methods indicated above are equal to each other. Thermodynamical parameters, NBO analysis data, and HOMO/LUMO images for this compound are also presented. A good agreement between the calculated data obtained using the above three quantum-chemical methods was noticed, too. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Open AccessArticle

3D Characterization of the Molecular Neighborhood of ^•OH Radical in High Temperature Water by MD Simulation and Voronoi Polyhedra

Lukasz Kazmierczak

Joanna Szala-Rearick

and

Dorota Swiatla-Wojcik

Int. J. Mol. Sci. 2023, 24(4), 3294; https://doi.org/10.3390/ijms24043294 - 07 Feb 2023

Viewed by 642

Abstract

Understanding the properties of the ^•OH radical in aqueous environments is essential for biochemistry, atmospheric chemistry, and the development of green chemistry technologies. In particular, the technological applications involve knowledge of microsolvation of the ^•OH radical in high temperature water. In this study, the classical molecular dynamics (MD) simulation and the technique based on the construction of Voronoi polyhedra were used to provide 3D characteristics of the molecular vicinity of the aqueous hydroxyl radical (^•OH_aq). The statistical distribution functions of metric and topological features of solvation shells represented by the constructed Voronoi polyhedra are reported for several thermodynamic states of water, including the pressurized high-temperature liquid and supercritical fluid. Calculations showed a decisive influence of the water density on the geometrical properties of the ^•OH solvation shell in the sub- and supercritical region: with the decreasing density, the span and asymmetry of the solvation shell increase. We also showed that the 1D analysis based on the oxygen–oxygen radial distribution functions (RDFs) overestimates the solvation number of ^•OH and insufficiently reflects the influence of transformations in the hydrogen-bonded network of water on the structure of the solvation shell. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Open AccessArticle

Microenvironmental Impact on InP/ZnS-Based Quantum Dots in In Vitro Models and in Living Cells: Spectrally- and Time-Resolved Luminescence Analysis

and

Int. J. Mol. Sci. 2023, 24(3), 2699; https://doi.org/10.3390/ijms24032699 - 31 Jan 2023

Viewed by 674

Abstract

Quantum dots (QDs) have attracted great attention as tools for theranostics that combine the possibility of simultaneous biological target visualization and medicine delivery. Here, we address whether core/shell InP/ZnS QDs (InP-QDs) may be an alternative to toxic Cd-based QDs. We analyze InP-QD photophysical characteristics in cell culture medium, salt solutions, and directly in the cells. It was demonstrated that InP-QDs were internalized into endolysosomes in HeLa and A549 cells with dynamics similar to Cd-based QDs of the same design, but the two cell lines accumulated them with different efficiencies. InP-QDs were reliably detected in the endosomes despite their low quantum yields. Cell culture medium efficiently decreased the InP-QD photoluminescence lifetime by 50%, acidic pH (4.0) had a moderate effect (20–25% reduction), and quenching by salt solutions typical of intra-endosomal medium composition resulted in a decrease of about 10–15%. The single-vesicle fluorescence-lifetime imaging microscopy analysis of QDs inside and outside the cells shows that the scatter between endosomes in the same cell can be significant, which indicates the complex impact of the abovementioned factors on the state of InP-QDs. The PI test and MTT test demonstrate that InP-QDs are toxic for both cell lines at concentrations higher than 20 nM. Possible reasons for InP-QD toxicity are discussed. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Open AccessArticle

Combined Fluorescence Fluctuation and Spectrofluorometric Measurements Reveal a Red-Shifted, Near-IR Emissive Photo-Isomerized Form of Cyanine 5

and

Int. J. Mol. Sci. 2023, 24(3), 1990; https://doi.org/10.3390/ijms24031990 - 19 Jan 2023

Cited by 1 | Viewed by 549

Abstract

Cyanine fluorophores are extensively used in fluorescence spectroscopy and imaging. Upon continuous excitation, especially at excitation conditions used in single-molecule and super-resolution experiments, photo-isomerized states of cyanines easily reach population probabilities of around 50%. Still, effects of photo-isomerization are largely ignored in such experiments. Here, we studied the photo-isomerization of the pentamethine cyanine 5 (Cy5) by two similar, yet complementary means to follow fluorophore blinking dynamics: fluorescence correlation spectroscopy (FCS) and transient-state (TRAST) excitation–modulation spectroscopy. Additionally, we combined TRAST and spectrofluorimetry (spectral-TRAST), whereby the emission spectra of Cy5 were recorded upon different rectangular pulse-train excitations. We also developed a framework for analyzing transitions between multiple emissive states in FCS and TRAST experiments, how the brightness of the different states is weighted, and what initial conditions that apply. Our FCS, TRAST, and spectral-TRAST experiments showed significant differences in dark-state relaxation amplitudes for different spectral detection ranges, which we attribute to an additional red-shifted, emissive photo-isomerized state of Cy5, not previously considered in FCS and single-molecule experiments. The photo-isomerization kinetics of this state indicate that it is formed under moderate excitation conditions, and its population and emission may thus deserve also more general consideration in fluorescence imaging and spectroscopy experiments. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Open AccessArticle

Regioselective Cycloaddition of Nitrile Imines to 5-Methylidene-3-phenyl-hydantoin: Synthesis and DFT Calculations

Maria E. Filkina

Daria N. Baray

Elena K. Beloglazkina

Yuri K. Grishin

Vitaly A. Roznyatovsky

and

Maxim E. Kukushkin

Int. J. Mol. Sci. 2023, 24(2), 1289; https://doi.org/10.3390/ijms24021289 - 09 Jan 2023

Cited by 1 | Viewed by 920

Abstract

Nitrile imine cycloaddition to hydantoins containing an exocyclic C=C double bond has been previously described in a very limited number of examples. In this work, regioselective synthesis of spiro-pyrazoline-imidazolidine-2,4-diones based on a 1,3-dipolar cycloaddition reaction of nitrile imines to 5-methylidene-3-phenyl-hydantoin have been proposed. It was found that, regardless of the nature of the aryl substituents at the terminal C and N atoms of the C-N-N fragment of nitrile imine (electron donor or electron acceptor), cycloaddition to the 5-methylidenhydantoin exocyclic C=C bond proceeds regioselectively, and the terminal nitrogen atom of the nitrile imine connects to the more sterically hindered carbon atom of the double bond, which leads to the formation of a 5-disubstituted pyrazoline ring. The observed cycloaddition regioselectivity was rationalized using DFT calculations of frontier molecular orbital interactions, global CDFT reactivity indices, and minimum energy paths. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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Review

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Open AccessReview

Recent Advances in the Preparation of Delivery Systems for the Controlled Release of Scents

Adrian Saura-Sanmartin

and

Laura Andreu-Ardil

Int. J. Mol. Sci. 2023, 24(5), 4685; https://doi.org/10.3390/ijms24054685 - 28 Feb 2023

Viewed by 1084

Abstract

Scents are volatile compounds highly employed in a wide range of manufactured items, such as fine perfumery, household products, and functional foods. One of the main directions of the research in this area aims to enhance the longevity of scents by designing efficient delivery systems to control the release rate of these volatile molecules and also increase their stability. Several approaches to release scents in a controlled manner have been developed in recent years. Thus, different controlled release systems have been prepared, including polymers, metal–organic frameworks and mechanically interlocked systems, among others. This review is focused on the preparation of different scaffolds to accomplish a slow release of scents, by pointing out examples reported in the last five years. In addition to discuss selected examples, a critical perspective on the state of the art of this research field is provided, comparing the different types of scent delivery systems. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2023)

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