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Feature Papers in ‘Physical Chemistry and Chemical Physics’: Fourth Edition

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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: 20 February 2026 | Viewed by 1389

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Prof. Dr. Dongho Kim

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Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, 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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Dear Colleagues,

This Special Issue of the International Journal of Molecular Sciences (IJMS) highlights new and original research that appeals to a broad audience across all aspects of physical chemistry and chemical physics. This issue invites research that offers significant innovations and insights in the fields of physical chemistry and chemical physics, with a focus on molecular research. The submitted articles will be judged by editors and peer reviewers. Topics include, but are not limited to, the following research areas:

Intermolecular forces that act upon the physical properties of materials;
Reaction kinetics on the rate of a reaction;
The identity of ions and the electrical conductivity of materials;
Surface science and the electrochemistry of cell membranes;
Probing the structure and dynamics of ions, free radicals, polymers, clusters, and molecules;
Chemical structures and reactions at the quantum mechanical level;
The structure and reactivity of gas-phase ions and radicals;
Energy/charge transfer dynamics in organic/inorganic materials;
Physical processes in nanomaterials.

Prof. Dr. Dongho Kim
Guest Editor

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Keywords

heterogeneous structures
alignment and surface phenomena
quantum theory
mathematical physics
statistical and classical mechanics
molecular structure
chemical kinetics
laser physics
dynamics
kinetics
photochemistry
spectroscopy
exciton dynamics
statistical mechanics
thermodynamics
electrochemistry
catalysis
surface science
quantum mechanics
theoretical developments
fundamental aspects of catalysis
solar energy conversion
polymer dynamics

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Published Papers (4 papers)

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12 pages, 1055 KB

Open AccessCommunication

5-Hydroxylysine Captures the Suicidally-Inactivated Conformational State of Lysine 5,6-Aminomutase

by Amarendra Nath Maity, Jun-Ru Chen, Ting-Xi Ke and Shyue-Chu Ke

Int. J. Mol. Sci. 2025, 26(17), 8561; https://doi.org/10.3390/ijms26178561 - 3 Sep 2025

Abstract

The ability of enzymes to access various conformational states is often essential for their catalytic activity. Lysine 5,6-aminomutase (5,6-LAM), a pyridoxal 5′-phosphate (PLP) and 5′-deoxyadenosylcobalamin (dAdoCbl)dependent enzyme, catalyzes 1,2-amino shift in lysine isomers by shuttling between an open conformational state and a closed conformational state. Nevertheless, suicide inactivation of 5,6-LAM is an obstacle to the realization of its potential as a biocatalyst. In this work, the fate of the reaction of 5-hydroxylysine, an analogue of lysine, is investigated using spectroscopic and computational methods. Although 5-hydroxylysine does not afford any product, results obtained from UV–visible and electron paramagnetic resonance (EPR) spectroscopies demonstrate that initial steps of the catalytic cycle are performed with it. Simulation of the weakly spin-coupled spectrum estimates an intermediate distance between the PLP substrate-based radical and Co(II) in comparison to the that in the open state and the closed state. This distinct conformational state, different from the open state and the closed state, is alluded to in its putative role in suicide inactivation and denoted as the suicidally-inactivated state. Our findings highlight the emergence of EPR spectroscopy as a powerful tool to uncover the hidden conformations in radical enzymes. These results provide new insights into the suicide inactivation of dAdoCbl-dependent enzymes. Full article

(This article belongs to the Special Issue Feature Papers in ‘Physical Chemistry and Chemical Physics’: Fourth Edition)

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21 pages, 7777 KB

Open AccessArticle

Physicochemical and Computational Study of the Encapsulation of Resv-4′-LA and Resv-4′-DHA Lipophenols by Natural and HP-β-CDs

by Ana Belén Hernández-Heredia, Dennis Alexander Silva-Cullishpuma, José Pedro Cerón-Carrasco, Ángel Gil-Izquierdo, Jordan Lehoux, Léo Faion, Céline Crauste, Thierry Durand, José Antonio Gabaldón and Estrella Núñez-Delicado

Int. J. Mol. Sci. 2025, 26(15), 7454; https://doi.org/10.3390/ijms26157454 - 1 Aug 2025

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Abstract

This study investigates the self-assembly and host–guest complexation behaviour of novel resveratrol-based lipophenols (LipoResv)—resveratrol-4′-linoleate (Resv-4′-LA) and resveratrol-4′-docosahexaenoate (Resv-4′-DHA)—with hydroxypropyl-β-cyclodextrins (HP-β-CDs). These amphiphilic molecules display surfactant-like properties, forming micellar aggregates in aqueous media. Fluorescence spectroscopy was used to determine the critical micelle concentration (CMC), revealing that LipoResv exhibit significantly lower CMC values than their free fatty acids, indicating higher hydrophobicity. The formation of inclusion complexes with HP-β-CDs was evaluated based on changes in CMC values and further confirmed by dynamic light scattering (DLS) and molecular modelling analyses. Resv-4′-LA formed 1:1 complexes (Kc = 720 M⁻¹), while Resv-4′-DHA demonstrated a 1:2 stoichiometry with lower affinity constants (K₁ = 17 M⁻¹, K₂ = 0.18 M⁻¹). Environmental parameters (pH, temperature, and ionic strength) significantly modulated CMC and binding constants. Computational docking and molecular dynamics simulations supported the experimental findings by revealing the key structural determinants of the host–guest affinity and micelle stabilization. Ligand efficiency (LE) analysis further aligned with the experimental data, favouring the unmodified fatty acids. These results highlight the versatile encapsulation capacity of HP-β-CDs for bioactive amphiphile molecules and support their potential applications in drug delivery and functional food systems. Full article

(This article belongs to the Special Issue Feature Papers in ‘Physical Chemistry and Chemical Physics’: Fourth Edition)

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17 pages, 7508 KB

Open AccessArticle

Supramolecular Graphene Quantum Dots/Porphyrin Complex as Fluorescence Probe for Metal Ion Sensing

by Mariachiara Sarà, Andrea Romeo, Gabriele Lando, Maria Angela Castriciano, Roberto Zagami, Giovanni Neri and Luigi Monsù Scolaro

Int. J. Mol. Sci. 2025, 26(15), 7295; https://doi.org/10.3390/ijms26157295 - 28 Jul 2025

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Abstract

Graphene quantum dots (GQDs) obtained by microwave-induced pyrolysis of glutamic acid and triethylenetetramine (trien) are fairly stable, emissive, water-soluble, and positively charged nano-systems able to interact with negatively charged meso-tetrakis(4-sulfonatophenyl) porphyrin (TPPS₄). The stoichiometric control during the preparation affords a supramolecular adduct, GQDs@TPPS₄, that exhibits a double fluorescence emission from both the GQDs and the TPPS₄ fluorophores. These supramolecular aggregates have an overall negative charge that is responsible for the condensation of cations in the nearby aqueous layer, and a three-fold acceleration of the metalation rates of Cu²⁺ ions has been observed with respect to the parent porphyrin. Addition of various metal ions leads to some changes in the UV/Vis spectra and has a different impact on the fluorescence emission of GQDs and TPPS₄. The quenching efficiency of the TPPS₄ emission follows the order Cu²⁺ > Hg²⁺ > Cd²⁺ > Pb²⁺ ~ Zn²⁺ ~ Co²⁺ ~ Ni²⁺ > Mn²⁺ ~ Cr³⁺ >> Mg²⁺ ~ Ca²⁺ ~ Ba²⁺, and it has been related to literature data and to the sitting-atop mechanism that large transition metal ions (e.g., Hg²⁺ and Cd²⁺) exhibit in their interaction with the macrocyclic nitrogen atoms of the porphyrin, inducing distortion and accelerating the insertion of smaller metal ions, such as Zn²⁺. For the most relevant metal ions, emission quenching of the porphyrin evidences a linear behavior in the micromolar range, with the emission of the GQDs being moderately affected through a filter effect. Deliberate pollution of the samples with Zn²⁺ reveals the ability of the GQDs@TPPS₄ adduct to detect sensitively Cu²⁺, Hg^2+, and Cd²⁺ ions. Full article

(This article belongs to the Special Issue Feature Papers in ‘Physical Chemistry and Chemical Physics’: Fourth Edition)

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18 pages, 2182 KB

Open AccessArticle

Assessment of Hydroxyl Radical Reactivity in Sulfur-Containing Amino Acid Models Under Acidic pH

by Chryssostomos Chatgilialoglu, Piotr Filipiak, Tomasz Szreder, Ireneusz Janik, Gordon L. Hug, Magdalena Grzelak, Franciszek Kazmierczak, Jerzy Smorawinski, Krzysztof Bobrowski and Bronislaw Marciniak

Int. J. Mol. Sci. 2025, 26(15), 7203; https://doi.org/10.3390/ijms26157203 - 25 Jul 2025

Viewed by 281

Abstract

Methionine residues in proteins and peptides are frequently oxidized by losing one electron. The presence of nearby amide groups is crucial for this process, enabling methionine to participate in long-range electron transfer. Hydroxyl radical (HO^•) plays an important role being generated in aerobic organisms by cellular metabolisms as well as by exogenous sources such as ionizing radiations. The reaction of HO^• with methionine mainly affords the one-electron oxidation of the thioether moiety through two consecutive steps (HO^• addition to the sulfur followed by HO⁻ elimination). We recently investigated the reaction of HO^• with model peptides mimicking methionine and its cysteine-methylated counterpart, i.e., CH₃C(O)NHCHXC(O)NHCH₃, where X = CH₂CH₂SCH₃ or CH₂SCH₃ at pH 7. The reaction mechanism varied depending on the distance between the sulfur atom and the peptide backbone, but, for a better understanding of various suggested equilibria, the analysis of the flux of protons is required. We extended the previous study to the present work at pH 4 using pulse radiolysis techniques with conductivity and optical detection of transient species, as well as analysis of final products by LC-MS and high-resolution MS/MS following γ-radiolysis. Comparing all the data provided a better understanding of how the presence of nearby amide groups influences the one-electron oxidation mechanism. Full article

(This article belongs to the Special Issue Feature Papers in ‘Physical Chemistry and Chemical Physics’: Fourth Edition)

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