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Feature Papers in 'Physical Chemistry and Chemical Physics' 2024

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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 2025 | Viewed by 11398

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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,

In this International Journal of Molecular Sciences (IJMS) Special Issue, new and original research that has a broad readership from all aspects of physical chemistry and chemical physics is published. For publication here, research must provide significant new innovations and insights in the physical chemistry and chemical physics fields with a focus on molecular research. The submitted articles will be judged by the Editors and peer-reviewers. Topics include, but are not limited to, the following:

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 etc

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Published Papers (10 papers)

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Research

18 pages, 3747 KiB

Open AccessArticle

On the Potential Energy Surface of the Pyrene Dimer

by Jiří Czernek and Jiří Brus

Int. J. Mol. Sci. 2024, 25(19), 10762; https://doi.org/10.3390/ijms251910762 - 6 Oct 2024

Viewed by 780

Abstract

Knowledge of reliable geometries and associated intermolecular interaction energy (ΔE) values at key fragments of the potential energy surface (PES) in the gas phase is indispensable for the modeling of various properties of the pyrene dimer (PYD) and other important aggregate systems of a comparatively large size (ca. 50 atoms). The performance of the domain-based local pair natural orbital (DLPNO) variant of the coupled-cluster theory with singles, doubles and perturbative triples in the complete basis set limit [CCSD(T)/CBS] method for highly accurate predictions of the ΔE at a variety of regions of the PES was established for a representative set of pi-stacked dimers, which also includes the PYD. For geometries with the distance between stacked monomers close to a value of such a distance in the ΔE minimum structure, an excellent agreement between the canonical CCSD(T)/CBS results and their DLPNO counterparts was found. This finding enabled us to accurately characterize the lowest-lying configurations of the PYD, and the physical origin of their stabilization was thoroughly analyzed. The proposed DLPNO-CCSD(T)/CBS procedure should be applied with the aim of safely locating a global minimum of the PES and firmly establishing the pertaining ΔE of even larger dimers in studies of packing motifs of organic electronic devices and other novel materials. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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15 pages, 6223 KiB

Open AccessArticle

Revisiting the Most Stable Structures of the Benzene Dimer

by Jiří Czernek and Jiří Brus

Int. J. Mol. Sci. 2024, 25(15), 8272; https://doi.org/10.3390/ijms25158272 - 29 Jul 2024

Cited by 1 | Viewed by 868

Abstract

The benzene dimer (BD) is an archetypal model of π∙∙∙π and C–H∙∙∙π noncovalent interactions as they occur in its cofacial and perpendicular arrangements, respectively. The enthalpic stabilization of the related BD structures has been debated for a long time and is revisited here. The revisit is based on results of computations that apply the coupled-cluster theory with singles, doubles and perturbative triples [CCSD(T)] together with large basis sets and extrapolate results to the complete basis set (CBS) limit in order to accurately characterize the three most important stationary points of the intermolecular interaction energy (ΔE) surface of the BD, which correspond to the tilted T-shaped (TT), fully symmetric T-shaped (FT) and slipped-parallel (SP) structures. In the optimal geometries obtained by searching extensive sets of the CCSD(T)/CBS ΔE data of the TT, FT and SP arrangements, the resulting ΔE values were −11.84, −11.34 and −11.21 kJ/mol, respectively. The intrinsic strength of the intermolecular bonding in these configurations was evaluated by analyzing the distance dependence of the CCSD(T)/CBS ΔE data over wide ranges of intermonomer separations. In this way, regions of the relative distances that favor BD structures with either π∙∙∙π or C–H∙∙∙π interactions were found and discussed in a broader context. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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13 pages, 1241 KiB

Open AccessArticle

Harmonic Generation in Molecular Ag₂S Plasma

by Rashid A. Ganeev

Int. J. Mol. Sci. 2024, 25(15), 8106; https://doi.org/10.3390/ijms25158106 - 25 Jul 2024

Viewed by 525

Abstract

The molecular laser-induced plasma (LIP) produced during the ablation of silver sulfide (Ag₂S) was used as a medium for high-order harmonic generation in the extreme ultraviolet range. The role of LIP formation, the plasma components, and the geometry of plasma in the harmonic conversion efficiency was analyzed. We also analyzed the influence of the driving pulses (chirp, single-color pump, two-color pump, and delay between heating and converting pulses) on the harmonic yield in Ag₂S LIP. The application of molecular plasma was compared with the application of atomic plasma, which comprised similar metallic elements (Ag) as well as other metal LIPs. The harmonics from the Ag₂S LIP were 4 to 10 times stronger than those from the Ag LIP. The harmonics up to the 59th order were achieved under the optimal conditions for the molecular plasma. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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17 pages, 3035 KiB

Open AccessArticle

A New Method for Growth Factor Enrichment from Dairy Products by Electrodialysis with Filtration Membranes: The Major Impact of Raw Product Pretreatment

by Sabita Kadel, Vladlen Nichka, Jacinthe Thibodeau, Behnaz Razi Parjikolaei and Laurent Bazinet

Int. J. Mol. Sci. 2024, 25(13), 7211; https://doi.org/10.3390/ijms25137211 - 29 Jun 2024

Viewed by 902

Abstract

This study is focused on fractionation of insulin-like growth factor I (IGF-I) and transforming growth factor-β2 (TGF-β2) using a new electro-based membrane process calledelectrodialysis with filtration membranes (EDFM). Before EDFM, different pretreatments were tested, and four pH conditions (4.25, 3.85, 3.45, and 3.05) were used during EDFM. It was demonstrated that a 1:1 dilution of defatted colostrum with deionized water to decrease mineral content followed by the preconcentration of GFs by UF is necessary and allow for these compounds to migrate to the recovery compartment during EDFM. MS analyses confirmed the migration, in low quantity, of only α-lactalbumin (α-la) and β-lactoglobulin (β-lg) from serocolostrum to the recovery compartment during EDFM. Consequently, the ratio of GFs to total protein in recovery compartment compared to that of feed serocolostrum solution was 60× higher at pH value 3.05, the optimal pH favoring the migration of IGF-I and TGF-β2. Finally, these optimal conditions were tested on acid whey to also demonstrate the feasibility of the proposed process on one of the main by-products of the cheese industry; the ratio of GFs to total protein was 2.7× higher in recovery compartment than in feed acid whey solution, and only α-la migrated. The technology of GF enrichment for different dairy solutions by combining ultrafiltration and electrodialysis technologies was proposed for the first time. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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12 pages, 1642 KiB

Open AccessArticle

PACSAB Server: A Web-Based Tool for the Study of Aggregation and the Conformational Ensemble of Disordered and Folded Proteins

by Agustí Emperador

Int. J. Mol. Sci. 2024, 25(11), 6021; https://doi.org/10.3390/ijms25116021 - 30 May 2024

Viewed by 644

Abstract

We present in this article the PACSAB server, which is designed to provide information about the structural ensemble and interactions of both stable and disordered proteins to researchers in the field of molecular biology. The use of this tool does not require any computational skills as the user just needs to upload the structure of the protein to be studied; the server runs a simulation with the PACSAB model, a highly accurate coarse-grained model that is much more efficient than standard molecular dynamics for the exploration of the conformational space of multiprotein systems. The trajectories generated by the simulations based on this model reveal the propensity of the protein under study for aggregation, identify the residues playing a central role in the aggregation process, and reproduce the whole conformational space of disordered proteins. All of this information is shown and can be downloaded from the web page. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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26 pages, 6567 KiB

Open AccessArticle

Dual Emissive Zn(II) Naphthalocyanines: Synthesis, Structural and Photophysical Characterization with Theory-Supported Insights towards Soluble Coordination Compounds with Visible and Near-Infrared Emission

by Sidharth Thulaseedharan Nair Sailaja, Iván Maisuls, Alexander Hepp, Dana Brünink, Nikos L. Doltsinis, Andreas Faust, Sven Hermann and Cristian A. Strassert

Int. J. Mol. Sci. 2024, 25(5), 2605; https://doi.org/10.3390/ijms25052605 - 23 Feb 2024

Viewed by 1130

Abstract

Metal phthalocyaninates and their higher homologues are recognized as deep-red luminophores emitting from their lowest excited singlet state. Herein, we report on the design, synthesis, and in-depth characterization of a new class of dual-emissive (visible and NIR) metal naphthalocyaninates. A 4-N,N-dimethylaminophen-4-yl-substituted naphthalocyaninato zinc(II) complex (Zn-NMe₂Nc) and the derived water-soluble coordination compound (Zn-NMe₃Nc) exhibit a near-infrared fluorescence from the lowest ligand-centered state, along with a unique push–pull-supported luminescence in the visible region of the electromagnetic spectrum. An unprecedentedly broad structural (2D-NMR spectroscopy and mass spectrometry) as well as photophysical characterization (steady-state state and time-resolved photoluminescence spectroscopy) is presented. The unique dual emission was assigned to two independent sets of singlet states related to the intrinsic Q-band of the macrocycle and to the push–pull substituents in the molecular periphery, respectively, as predicted by TD-DFT calculations. In general, the elusive chemical aspects of these macrocyclic compounds are addressed, involving both reaction conditions, thorough purification, and in-depth characterization. Besides the fundamental aspects that are investigated herein, the photoacoustic properties were exemplarily examined using phantom gels to assess their tomographic imaging capabilities. Finally, the robust luminescence in the visible range arising from the push–pull character of the peripheral moieties demonstrated a notable independence from aggregation and was exemplarily implemented for optical imaging (FLIM) through time-resolved multiphoton micro(spectro)scopy. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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21 pages, 2729 KiB

Open AccessArticle

Synthesis and Biological Evaluation of Novel Amino and Amido Substituted Pentacyclic Benzimidazole Derivatives as Antiproliferative Agents

by Nataša Perin, Marjana Gulin, Marija Kos, Leentje Persoons, Dirk Daelemans, Ivana Fabijanić, Marijana Radić Stojković and Marijana Hranjec

Int. J. Mol. Sci. 2024, 25(4), 2288; https://doi.org/10.3390/ijms25042288 - 14 Feb 2024

Viewed by 1371

Abstract

Newly designed pentacyclic benzimidazole derivatives featuring amino or amido side chains were synthesized to assess their in vitro antiproliferative activity. Additionally, we investigated their direct interaction with nucleic acids, aiming to uncover potential mechanisms of biological action. These compounds were prepared using conventional organic synthesis methodologies alongside photochemical and microwave-assisted reactions. Upon synthesis, the newly derived compounds underwent in vitro testing for their antiproliferative effects on various human cancer cell lines. Notably, derivatives 6 and 9 exhibited significant antiproliferative activity within the submicromolar concentration range. The biological activity was strongly influenced by the N atom’s position on the quinoline moiety and the position and nature of the side chain on the pentacyclic skeleton. Findings from fluorescence, circular dichroism spectroscopy, and thermal melting assays pointed toward a mixed binding mode—comprising intercalation and the binding of aggregated compounds along the polynucleotide backbone—of these pentacyclic benzimidazoles with DNA and RNA. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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15 pages, 3358 KiB

Open AccessArticle

A Kinetic Investigation of the Supramolecular Chiral Self-Assembling Process of Cationic Organometallic (2,2′:6′,2″-terpyridine)methylplatinum(II) Complexes with Poly(L-glutamic Acid)

by Maria Angela Castriciano, Roberto Zagami, Antonino Mazzaglia, Andrea Romeo and Luigi Monsù Scolaro

Int. J. Mol. Sci. 2024, 25(2), 1176; https://doi.org/10.3390/ijms25021176 - 18 Jan 2024

Cited by 1 | Viewed by 839

Abstract

The cationic platinum(II) organometallic complex [Pt(terpy)Me]⁺ (terpy = 2,2′:6′,2″-terpyridine) at mild acidic pH interacts with poly(L-glutamic acid) (L-PGA) in its α-helix conformation, affording chiral supramolecular adducts. Their kinetics of formation have been investigated in detail as a function of the concentrations of both reagents and changing pH, ionic strength, the length of the polymeric scaffold and temperature. After a very fast early stage, the kinetic traces have been analyzed as three consecutive steps, suggesting a mechanism based on the electrostatic fast formation of a not-organized aggregate that subsequently evolves through different rearrangements to form the eventual supramolecular adduct. A model for this species has been proposed based on (i) the attractive electrostatic interaction of the cationic platinum(II) complexes and the polyelectrolyte and (ii) the π-stacking interactions acting among the [Pt(terpy)Me]⁺ units. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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25 pages, 4676 KiB

Open AccessArticle

Gas-Phase vs. Grain-Surface Formation of Interstellar Complex Organic Molecules: A Comprehensive Quantum-Chemical Study

by Berta Martínez-Bachs and Albert Rimola

Int. J. Mol. Sci. 2023, 24(23), 16824; https://doi.org/10.3390/ijms242316824 - 27 Nov 2023

Cited by 4 | Viewed by 1683

Abstract

Several organic chemical compounds (the so-called interstellar complex organic molecules, iCOMs) have been identified in the interstellar medium (ISM). Examples of iCOMs are formamide (HCONH₂), acetaldehyde (CH₃CHO), methyl formate (CH₃OCHO), or formic acid (HCOOH). iCOMs can serve as precursors of other organic molecules of enhanced complexity, and hence they are key species in chemical evolution in the ISM. The formation of iCOMs is still a subject of a vivid debate, in which gas-phase or grain-surface syntheses have been postulated. In this study, we investigate the grain-surface-formation pathways for the four above-mentioned iCOMs by transferring their primary gas-phase synthetic routes onto water ice surfaces. Our objective is twofold: (i) to identify potential grain-surface-reaction mechanisms leading to the formation of these iCOMs, and (ii) to decipher either parallelisms or disparities between the gas-phase and the grain-surface reactions. Results obtained indicate that the presence of the icy surface modifies the energetic features of the reactions compared to the gas-phase scenario, by increasing some of the energy barriers. Therefore, the investigated gas-phase mechanisms seem unlikely to occur on the icy grains, highlighting the distinctiveness between the gas-phase and the grain-surface chemistry. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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16 pages, 11914 KiB

Open AccessArticle

Organelle Imaging with Terahertz Scattering-Type Scanning Near-Field Microscope

by Jie Huang, Jie Wang, Linghui Guo, Dianxing Wu, Shihan Yan, Tianying Chang and Hongliang Cui

Int. J. Mol. Sci. 2023, 24(17), 13630; https://doi.org/10.3390/ijms241713630 - 4 Sep 2023

Cited by 2 | Viewed by 1575

Abstract

Organelles play core roles in living beings, especially in internal cellular actions, but the hidden information inside the cell is difficult to extract in a label-free manner. In recent years, terahertz (THz) imaging has attracted much attention because of its penetration depth in nonpolar and non-metallic materials and label-free, non-invasive and non-ionizing ability to obtain the interior information of bio-samples. However, the low spatial resolution of traditional far-field THz imaging systems and the weak dielectric contrast of biological samples hinder the application of this technology in the biological field. In this paper, we used an advanced THz scattering near-field imaging method for detecting chloroplasts on gold substrate with nano-flatness combined with an image processing method to remove the background noise and successfully obtained the subcellular-grade internal reticular structure from an Arabidopsis chloroplast THz image. In contrast, little inner information could be observed in the tea chloroplast in similar THz images. Further, transmission electron microscopy (TEM) and mass spectroscopy (MS) were also used to detect structural and chemical differences inside the chloroplasts of Arabidopsis and tea plants. The preliminary results suggested that the interspecific different THz information is related to the internal spatial structures of chloroplasts and metabolite differences among species. Therefore, this method could open a new way to study the structure of individual organelles. Full article

(This article belongs to the Special Issue Feature Papers in 'Physical Chemistry and Chemical Physics' 2024)

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