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Search Results (610)

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Keywords = quantum-chemical investigations

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11 pages, 950 KiB  
Article
Numerical Investigation on the Thomas–Fermi Model and Its Quantum and Exchange Corrections
by Yangyang Ma, Wenle Song, Junlei Zhao, Lei Wang, Shenghui Mu and Kun Wang
Plasma 2025, 8(3), 31; https://doi.org/10.3390/plasma8030031 (registering DOI) - 7 Aug 2025
Abstract
The Thomas–Fermi model and its quantum and exchange corrections with mathematic manipulations and numerical approaches are primarily investigated. The reduced ideal electron chemical potential is adopted as the initial value for the iterative solution of the Thomas–Fermi model. A new transformation for the [...] Read more.
The Thomas–Fermi model and its quantum and exchange corrections with mathematic manipulations and numerical approaches are primarily investigated. The reduced ideal electron chemical potential is adopted as the initial value for the iterative solution of the Thomas–Fermi model. A new transformation for the quantum and exchange equations is proposed to apply the boundary conditions easily. Both the Thomas–Fermi equation and correction equations are solved with the Runge–Kutta algorithm. The mathematical difficulties in controlling the computing accuracy of the equations containing the Fermi–Dirac integral are settled. The equation of state, based on the Thomas–Fermi model with its quantum and exchange corrections, is constructed and compared with relevant data. Full article
(This article belongs to the Special Issue New Insights into Plasma Theory, Modeling and Predictive Simulations)
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26 pages, 3951 KiB  
Article
Exploring the Bioactive Potential and Chemical Profile of Schinus molle Essential Oil: An Integrated In Silico and In Vitro Evaluation
by Rómulo Oses, Matías Ferrando, Flavia Bruna, Patricio Retamales, Myriam Navarro, Katia Fernández, Waleska Vera, María José Larrazábal, Iván Neira, Adrián Paredes, Manuel Osorio, Osvaldo Yáñez, Martina Jacobs and Jessica Bravo
Plants 2025, 14(15), 2449; https://doi.org/10.3390/plants14152449 - 7 Aug 2025
Abstract
Chilean Schinus molle has been used in traditional medicine for effects such as antibacterial, antifungal, anti-inflammatory, analgesic, antiviral, antitumoral, antioxidant, antispasmodic, astringent, antipyretic, cicatrizant, cytotoxic, diuretic, among others. In this study, we evaluated the pharmacological potential of Schinus molle seed essential oil extract [...] Read more.
Chilean Schinus molle has been used in traditional medicine for effects such as antibacterial, antifungal, anti-inflammatory, analgesic, antiviral, antitumoral, antioxidant, antispasmodic, astringent, antipyretic, cicatrizant, cytotoxic, diuretic, among others. In this study, we evaluated the pharmacological potential of Schinus molle seed essential oil extract (SM_EO) through in vitro and in silico approaches. In vitro, the antioxidant potential was analyzed, and antitumor activity was evaluated in non-tumor and human epithelial tumor cell lines. Caenorhabditis elegans was used as a model for evaluating toxicity, and the chemical composition of the SM_EO was analyzed using gas chromatography–mass spectrometry. The oil contained four major monoterpenes: α-phellandrene (34%), β-myrcene (23%), limonene (13%), and β-phellandrene (7%). Based on quantum mechanical calculations, the reactivity of the molecules present in the SM_EO was estimated. The results indicated that α- phellandrene, β-phellandrene, and β-myrcene showed the highest nucleophilic activity. In addition, the compounds following these as candidates for antioxidant and antiproliferative activities were α-phellandrene, β-phellandrene, ρ-cymene, sabinene, caryophyllene, l-limonene, and α-pinene, highlighting β-myrcene. Based on ADME-Tox properties, it is feasible to use these compounds as new drug candidates. Moreover, the antibacterial activity MIC value obtained for B. cereus was equivalent to 2 μg/mL, and for Y. enterocolitica, S. enteritidis, and S. typhimurium, the MIC value was 32.5 μg/μL. SM_EO could selectively inhibit the proliferation of human epithelial mammary tumor MCF7 cells treated with SM_EOs at 64 and 16 ug/mL—a significant increase in BCL-2 in a dose-dependent manner—and showed low toxicity against Caenorhabditis elegans (from 10 to 0.078 mg·mL−1). These findings suggest that SM_EO may be a potential source of bioactive compounds, encouraging further investigation for applications in veterinary medicine, cosmetics, and sanitation. Full article
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20 pages, 1523 KiB  
Article
Structural and Vibrational Characterizations of Alizarin Red S
by César A. N. Catalán, Licínia L. G. Justino, Rui Fausto, Gulce O. Ildiz and Silvia Antonia Brandán
Molecules 2025, 30(15), 3286; https://doi.org/10.3390/molecules30153286 - 5 Aug 2025
Abstract
In this work, the structures of the isolated anion and anhydrous and monohydrated sodium salts of alizarin red S (ARS) have been theoretically investigated within the density functional theory framework (B3LYP/6-311++G** calculations). The combination of calculations with the scaled quantum mechanics force field [...] Read more.
In this work, the structures of the isolated anion and anhydrous and monohydrated sodium salts of alizarin red S (ARS) have been theoretically investigated within the density functional theory framework (B3LYP/6-311++G** calculations). The combination of calculations with the scaled quantum mechanics force field (SQMFF) methodology has allowed the assignment of the experimental infrared spectrum of ARS in the solid phase and the determination of the corresponding force constants. The structural analysis also included the investigation of the NMR and UV-visible spectra of the compound in solution in light of the undertaken quantum chemical calculations, the obtained theoretical data being in good agreement with the corresponding experimental ones. The impact of the presence of the Na+ counterion and hydration water on the properties of the organic ARS fragment was evaluated. Atoms in molecules theory (AIM) analysis was also undertaken to obtain further details on the electronic structure of the investigated species, and the HOMO-LUMO gap was determined to evaluate their relative reactivity. Globally, the results obtained in this work extend the available information on alizarin red S and may also be used for the fast identification of the three studied species of the compound investigated (anhydrous and monohydrated sodium salts and isolated anion). Full article
(This article belongs to the Section Molecular Structure)
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20 pages, 2093 KiB  
Review
A Practical Guide Paper on Bulk and PLD Thin-Film Metals Commonly Used as Photocathodes in RF and SRF Guns
by Alessio Perrone, Muhammad Rizwan Aziz, Francisco Gontad, Nikolaos A. Vainos and Anna Paola Caricato
Chemistry 2025, 7(4), 123; https://doi.org/10.3390/chemistry7040123 - 30 Jul 2025
Viewed by 330
Abstract
This paper serves as a comprehensive and practical resource to guide researchers in selecting suitable metals for use as photocathodes in radio-frequency (RF) and superconducting radio-frequency (SRF) electron guns. It offers an in-depth review of bulk and thin-film metals commonly employed in many [...] Read more.
This paper serves as a comprehensive and practical resource to guide researchers in selecting suitable metals for use as photocathodes in radio-frequency (RF) and superconducting radio-frequency (SRF) electron guns. It offers an in-depth review of bulk and thin-film metals commonly employed in many applications. The investigation includes the photoemission, optical, chemical, mechanical, and physical properties of metallic materials used in photocathodes, with a particular focus on key performance parameters such as quantum efficiency, operational lifetime, chemical inertness, thermal emittance, response time, dark current, and work function. In addition to these primary attributes, this study examines essential parameters such as surface roughness, morphology, injector compatibility, manufacturing techniques, and the impact of chemical environmental factors on overall performance. The aim is to provide researchers with detailed insights to make well-informed decisions on materials and device selection. The holistic approach of this work associates, in tabular format, all photo-emissive, optical, mechanical, physical, and chemical properties of bulk and thin-film metallic photocathodes with experimental data, aspiring to provide unique tools for maximizing the effectiveness of laser cleaning treatment. Full article
(This article belongs to the Section Electrochemistry and Photoredox Processes)
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16 pages, 3308 KiB  
Article
Photocatalytic Degradation of Typical Fibrates by N and F Co-Doped TiO2 Nanotube Arrays Under Simulated Sunlight Irradiation
by Xiangyu Chen, Hao Zhong, Juanjuan Yao, Jingye Gan, Haibing Cong and Tengyi Zhu
Water 2025, 17(15), 2261; https://doi.org/10.3390/w17152261 - 29 Jul 2025
Viewed by 271
Abstract
Fibrate pharmaceuticals (fibrates), as a widespread class of emerging contaminants, pose potential risks to both ecological systems and human health. The photocatalytic system based on nitrogen (N) and fluorine (F) co-doped TiO2 nanotube arrays (NF-TNAs) provides a renewable solution for fibrate pharmaceutical [...] Read more.
Fibrate pharmaceuticals (fibrates), as a widespread class of emerging contaminants, pose potential risks to both ecological systems and human health. The photocatalytic system based on nitrogen (N) and fluorine (F) co-doped TiO2 nanotube arrays (NF-TNAs) provides a renewable solution for fibrate pharmaceutical removal from water, powered by inexhaustible sunlight. In this study, the degradation of two typical fibrates, i.e., bezafibrate (BZF) and ciprofibrate (CPF), under simulated sunlight irradiation through NF-TNAs were investigated. The photocatalytic degradation of BZF/CPF was achieved through combined radical and non-radical oxidation processes, while the generation and reaction mechanisms of associated reactive oxygen species (ROS) were examined. Electron paramagnetic resonance detection and quenching tests confirmed the existence of h+, •OH, O2•−, and 1O2, with O2•− playing the predominant role. The transformation products (TPs) of BZF/CPF were identified through high-resolution mass spectrometry analysis combined with quantum chemical calculations to elucidate the degradation pathways. The influence of co-existing ions and typical natural organic matters (NOM) on BZF/CPF degradation were also tested. Eventually, the ecological risk of BZF/CPF transformation products was assessed through quantitative structure–activity relationship (QSAR) modeling, and the results showed that the proposed photocatalytic system can largely alleviate fibrate toxicity. Full article
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13 pages, 4956 KiB  
Article
The Influence of Crystal Anisotropy in Femtosecond Laser Processing of Single-Crystal Diamond
by Guolong Wang, Ji Wang, Kaijie Cheng, Kun Yang, Bojie Xu, Wenbo Wang and Wenwu Zhang
Nanomaterials 2025, 15(15), 1160; https://doi.org/10.3390/nano15151160 - 28 Jul 2025
Viewed by 329
Abstract
The single-crystal diamond (SCD), owing to its extreme physical and chemical properties, serves as an ideal substrate for quantum sensing and high-frequency devices. However, crystal anisotropy imposes significant challenges on fabricating high-quality micro-nano structures, directly impacting device performance. This work investigates the effects [...] Read more.
The single-crystal diamond (SCD), owing to its extreme physical and chemical properties, serves as an ideal substrate for quantum sensing and high-frequency devices. However, crystal anisotropy imposes significant challenges on fabricating high-quality micro-nano structures, directly impacting device performance. This work investigates the effects of femtosecond laser processing on the SCD under two distinct crystallographic orientations via single-pulse ablation. The results reveal that ablation craters along the <100> orientation exhibit an elliptical shape with the major axis parallel to the laser polarization, whereas those along the <110> orientation form near-circular craters with the major axis at a 45° angle to the polarization. The single-pulse ablation threshold of the SCD along <110> is 9.56 J/cm2, representing a 7.8% decrease compared to 10.32 J/cm2 for <100>. The graphitization threshold shows a more pronounced reduction, dropping from 4.79 J/cm2 to 3.31 J/cm2 (31% decrease), accompanied by enhanced sp2 carbon order evidenced by the significantly intensified G-band in the Raman spectra. In addition, a phase transition layer of amorphous carbon at the nanoscale in the surface layer (thickness of ~40 nm) and a narrow lattice spacing of 0.36 nm are observed under TEM, corresponding to the interlayer (002) plane of graphite. These observations are attributed to the orientation-dependent energy deposition efficiency. Based on these findings, an optimized crystallographic orientation selection strategy for femtosecond laser processing is proposed to improve the quality of functional micro-nano structures in the SCD. Full article
(This article belongs to the Special Issue Trends and Prospects in Laser Nanofabrication)
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19 pages, 3715 KiB  
Article
Quantum Chemical Investigation on the Material Properties of Al-Based Hydrides XAl2H2 (X = Ca, Sr, Sc, and Y) for Hydrogen Storage Applications
by Yong Guo, Rui Guo, Lei Wan and Youyu Zhang
Materials 2025, 18(15), 3521; https://doi.org/10.3390/ma18153521 - 27 Jul 2025
Viewed by 319
Abstract
Aluminum–hydrogen compounds have drawn considerable interest for applications in solid-state hydrogen storage. The structural, hydrogen storage, electronic, mechanical, phonon, and thermodynamic properties of XAl2H2 (X = Ca, Sr, Sc, Y) hydrides are investigated using density functional theory. These hydrides exhibit [...] Read more.
Aluminum–hydrogen compounds have drawn considerable interest for applications in solid-state hydrogen storage. The structural, hydrogen storage, electronic, mechanical, phonon, and thermodynamic properties of XAl2H2 (X = Ca, Sr, Sc, Y) hydrides are investigated using density functional theory. These hydrides exhibit negative formation energies in the hexagonal phase, indicating their thermodynamic stability. The gravimetric hydrogen storage capacities of CaAl2H2, SrAl2H2, ScAl2H2, and YAl2H2 are calculated to be 1.41 wt%, 0.94 wt%, 1.34 wt%, and 0.93 wt%, respectively. Analysis of the electronic density of states reveals metallic characteristics. Furthermore, the calculated elastic constants satisfy the Born stability criteria, confirming their mechanical stability. Additionally, through phonon spectra analysis, dynamical stability is verified for CaAl2H2 and SrAl2H2 but not for ScAl2H2 and YAl2H2. Finally, we present temperature-dependent thermodynamic properties. This research reveals that XAl2H2 (X = Ca, Sr, Sc, Y) materials represent promising candidates for solid-state hydrogen storage, providing a theoretical foundation for further studies on XAl2H2 systems. Full article
(This article belongs to the Section Energy Materials)
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19 pages, 1941 KiB  
Article
Structural, Quantum Chemical, and Cytotoxicity Analysis of Acetylplatinum(II) Complexes with PASO2 and DAPTA Ligands
by Stefan Richter, Dušan Dimić, Milena R. Kaluđerović, Fabian Mohr and Goran N. Kaluđerović
Inorganics 2025, 13(8), 253; https://doi.org/10.3390/inorganics13080253 - 27 Jul 2025
Viewed by 428
Abstract
The development of novel platinum-based anticancer agents remains a critical objective in medicinal inorganic chemistry, particularly in light of resistance and toxicity limitations associated with cisplatin. In this study, the synthesis, structural characterization, quantum chemical analysis, and cytotoxic evaluation of four new acetylplatinum(II) [...] Read more.
The development of novel platinum-based anticancer agents remains a critical objective in medicinal inorganic chemistry, particularly in light of resistance and toxicity limitations associated with cisplatin. In this study, the synthesis, structural characterization, quantum chemical analysis, and cytotoxic evaluation of four new acetylplatinum(II) complexes (cis-[Pt(COMe)2(PASO2)2], cis-[Pt(COMe)2(DAPTA)2], trans-[Pt(COMe)Cl(DAPTA)2], and trans-[Pt(COMe)Cl(PASO2)]: 14, respectively) bearing cage phosphine ligands PASO2 (2-thia-1,3,5-triaza-phosphaadamantane 2,2-dioxide) and DAPTA (3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane) are presented. The coordination geometries and NMR spectral features of the cis/trans isomers were elucidated through multinuclear NMR and DFT calculations at the B3LYP/6-311++G(d,p)/LanL2DZ level, with strong agreement between experimental and theoretical data. Quantum Theory of Atoms in Molecules (QTAIM) analysis was applied to investigate bonding interactions and assess the covalent character of Pt–ligand bonds. Cytotoxicity was evaluated against five human cancer cell lines. The PASO2-containing complex in cis-configuration, 1, demonstrated superior activity against thyroid (8505C) and head and neck (A253) cancer cells, with potency surpassing that of cisplatin. The DAPTA complex 2 showed enhanced activity toward ovarian (A2780) cancer cells. These findings highlight the influence of ligand structure and isomerism on biological activity, supporting the rational design of phosphine-based Pt(II) anticancer drugs. Full article
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17 pages, 1725 KiB  
Article
Ring Opening upon Valence Shell Excitation in β-Butyrolactone: Experimental and Theoretical Methods
by Pedro A. S. Randi, Márcio H. F. Bettega, Nykola C. Jones, Søren V. Hoffmann, Małgorzata A. Śmiałek and Paulo Limão-Vieira
Molecules 2025, 30(15), 3137; https://doi.org/10.3390/molecules30153137 - 26 Jul 2025
Viewed by 269
Abstract
The valence-shell electronic state spectroscopy of β-butyrolactone (CH3CHCH2CO2) is comprehensively investigated by employing experimental and theoretical methods. We report a novel vacuum ultraviolet (VUV) absorption spectrum in the photon wavelength range from 115 to 320 nm (3.9–10.8 [...] Read more.
The valence-shell electronic state spectroscopy of β-butyrolactone (CH3CHCH2CO2) is comprehensively investigated by employing experimental and theoretical methods. We report a novel vacuum ultraviolet (VUV) absorption spectrum in the photon wavelength range from 115 to 320 nm (3.9–10.8 eV), together with ab initio quantum chemical calculations at the time-dependent density functional (TD-DFT) level of theory. The dominant electronic excitations are assigned to mixed valence-Rydberg and Rydberg transitions. The fine structure in the CH3CHCH2CO2 photoabsorption spectrum has been assigned to C=O stretching, v7a, CH2 wagging, v14a, C–O stretching, v22a, and C=O bending, v26a modes. Photolysis lifetimes in the Earth’s atmosphere from 0 km up to 50 km altitude have been estimated, showing to be a non-relevant sink mechanism compared to reactions with the OH radical. The nuclear dynamics along the C=O and C–C–C coordinates have been investigated at the TD-DFT level of theory, where, upon electronic excitation, the potential energy curves show important carbonyl bond breaking and ring opening, respectively. Within such an intricate molecular landscape, the higher-lying excited electronic states may keep their original Rydberg character or may undergo Rydberg-to-valence conversion, with vibronic coupling as an important mechanism contributing to the spectrum. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory (DFT) Calculation)
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20 pages, 2542 KiB  
Article
Rarefied Reactive Gas Flows over Simple and Complex Geometries Using an Open-Source DSMC Solver
by Rodrigo Cassineli Palharini, João Luiz F. Azevedo and Diego Vera Sepúlveda
Aerospace 2025, 12(8), 651; https://doi.org/10.3390/aerospace12080651 - 23 Jul 2025
Viewed by 234
Abstract
During atmospheric reentry, a significant number of chemical reactions are produced inside the high-temperature shock wave formed upstream of the spacecraft. Chemical reactions can significantly alter the flowfield structure surrounding the vehicle and affect surface properties, including heat transfer, pressure, and skin friction [...] Read more.
During atmospheric reentry, a significant number of chemical reactions are produced inside the high-temperature shock wave formed upstream of the spacecraft. Chemical reactions can significantly alter the flowfield structure surrounding the vehicle and affect surface properties, including heat transfer, pressure, and skin friction coefficients. In this scenario, the primary goal of this investigation is to evaluate the Quantum-Kinetic chemistry model for computing rarefied reactive gas flow over simple and complex geometries. The results are compared with well-established reaction models available for the transitional flow regime. The study focuses on two configurations, a sphere and the Orion capsule, analyzed at different altitudes to assess the impact of chemical nonequilibrium across varying flow rarefaction levels. Including chemical reactions led to lower post-shock temperatures, broader shock structures, and significant species dissociation in both geometries. These effects strongly influenced the surface heat flux, pressure, and temperature distributions. Comparison with results from the literature confirmed the validity of the implemented QK model and highlighted the importance of including chemical kinetics when simulating hypersonic flows in the upper atmosphere. Full article
(This article belongs to the Special Issue Thermal Protection System Design of Space Vehicles)
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12 pages, 878 KiB  
Article
Ustisorbicillinols G and H, Two New Antibacterial Sorbicillinoids from the Albino Strain LN02 of Rice False Smut Fungus Villosiclava virens
by Xuwen Hou, Mengyao Xue, Gan Gu, Dan Xu, Daowan Lai and Ligang Zhou
Molecules 2025, 30(14), 3039; https://doi.org/10.3390/molecules30143039 - 20 Jul 2025
Viewed by 313
Abstract
Villosiclava virens (anamorph: Ustilaginoidea virens), the causal fungal pathogen of rice false smut, has been found to produce various secondary metabolites. The albino strain LN02 is a natural albino phenotype mutant of V. virens due to its inability to produce ustilaginoidins. The [...] Read more.
Villosiclava virens (anamorph: Ustilaginoidea virens), the causal fungal pathogen of rice false smut, has been found to produce various secondary metabolites. The albino strain LN02 is a natural albino phenotype mutant of V. virens due to its inability to produce ustilaginoidins. The fermentation of V. virens LN02 was performed in solid rice medium to obtain fungal cultures, which were chemically investigated. After removing the known metabolites, two new dimeric sorbicillinoids, namely ustisorbicillinols G (1) and H (2), were isolated from the ethyl acetate extract. Their structures were elucidated using spectroscopic data analyses and quantum chemical calculations. Compounds 1 and 2 displayed antibacterial activity towards Ralstonia solanacearum, Agrobacterium tumefaciens and Bacillus subtilis, with median inhibitory concentration (IC50) values of 19.76–25.43 μg/mL for 1 and 25.35–45.48 μg/mL for 2. The discovery of new sorbicillinoids will increase the diversity of the secondary metabolites of V. virens and provide candidates for the creation of new antimicrobials as well. Full article
(This article belongs to the Special Issue Novel Antimicrobial Molecules Derived from Natural Sources)
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16 pages, 4966 KiB  
Article
Electrical–Thermal Aging Performance of PAH-Modified Interfacial Coating Agent for HVDC Cable Accessory
by Wenbo Zhu, Kaulya Pathiraja, Xu Guo, Baojun Hui, Mingli Fu, Linjie Zhao, Yuhuai Wang and Jin Li
Energies 2025, 18(14), 3767; https://doi.org/10.3390/en18143767 - 16 Jul 2025
Viewed by 331
Abstract
A novel interfacial coating agent was developed by modifying silicone oil with polycyclic aromatic hydrocarbons (PAHs) to enhance the insulation performance of HVDC cable accessories. This study investigates the effects of corona and hot–cold cycle aging on the DC breakdown characteristics of the [...] Read more.
A novel interfacial coating agent was developed by modifying silicone oil with polycyclic aromatic hydrocarbons (PAHs) to enhance the insulation performance of HVDC cable accessories. This study investigates the effects of corona and hot–cold cycle aging on the DC breakdown characteristics of the Cross-Linked Poly Ethylene and Ethylene Propylene Diene Monomer (XLPE/EPDM) interface. Interfacial breakdown tests, infrared spectroscopy, and a microstructural analysis were employed to investigate aging mechanisms. The results show that PAH-modified silicone oil significantly increases the breakdown voltage, with 2,4-dihydroxybenzophenone (C13H10O3) identified as the optimal additive via quantum chemical calculations (QCCs). Even after aging, the modified interface maintains its superior performance, confirming the long-term reliability of the coating. Full article
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14 pages, 2226 KiB  
Article
Investigation of the Effect of C-Terminal Adjacent Phenylalanine Residues on Asparagine Deamidation by Quantum Chemical Calculations
by Koichi Kato, Haruka Asai, Tomoki Nakayoshi, Ayato Mizuno, Akifumi Oda and Yoshinobu Ishikawa
Int. J. Mol. Sci. 2025, 26(14), 6819; https://doi.org/10.3390/ijms26146819 - 16 Jul 2025
Viewed by 214
Abstract
The deamidation rate is relatively high for Asn residues with Phe as the C-terminal adjacent residue in γS-crystallin, which is one of the human crystalline lens proteins. However, peptide-based experiments indicated that bulky amino acid residues on the C-terminal side impaired Asn deamination. [...] Read more.
The deamidation rate is relatively high for Asn residues with Phe as the C-terminal adjacent residue in γS-crystallin, which is one of the human crystalline lens proteins. However, peptide-based experiments indicated that bulky amino acid residues on the C-terminal side impaired Asn deamination. In this study, we hypothesized that the side chain of Phe affects the Asn deamidation rate and investigated the succinimide formation process using quantum chemical calculations. The B3LYP density functional theory was used to obtain optimized geometries of energy minima and transition states, and MP2 and M06-2X calculations were used to obtain the single-point energy. Activation barriers and rate-determining step changed depending on the orientation of the Phe side chain. In pathways where an interaction occurred between the benzene ring and the amide group of the Asn residue, the activation barrier was lower than in pathways where this interaction did not occur. Since the aromatic ring is oriented toward the Asn side in experimentally determined structures of γS-crystallin, the above interaction is considered to enhance the Asn deamidation. Full article
(This article belongs to the Section Molecular Biophysics)
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30 pages, 11919 KiB  
Article
Unveiling Vibrational Couplings in Model Peptides in Solution by a Theoretical Approach
by Federico Coppola, Fulvio Perrella, Alessio Petrone, Greta Donati, Luciana Marinelli and Nadia Rega
Molecules 2025, 30(13), 2854; https://doi.org/10.3390/molecules30132854 - 4 Jul 2025
Viewed by 446
Abstract
Vibrational analysis of peptides in solution and the theoretical determination of the effects of the microenvironment on infrared and Raman spectra are of key importance in many fields of chemical interest. In this work, we present a computational study combining static quantum mechanical [...] Read more.
Vibrational analysis of peptides in solution and the theoretical determination of the effects of the microenvironment on infrared and Raman spectra are of key importance in many fields of chemical interest. In this work, we present a computational study combining static quantum mechanical calculations with ab initio molecular dynamics simulations to investigate the vibrational behavior of three peptide models in both the gas phase and in explicit water, under non-periodic boundary conditions. The vibrational spectra of the main amide bands, namely amide I-III and A, were analyzed using a time–frequency approach based on the wavelet transform, which allows the resolution of transient frequency shifts and mode couplings along the trajectories. This combined approach enabled us to perform a time-resolved vibrational analysis revealing how vibrational frequencies, especially of the C=O and N–H stretching modes, evolve over time due to dynamical microsolvation. These fluctuations modulate vibrational couplings and lead to spectral broadening and frequency shifts that correlate with the local structuring of the solvent. In conclusion, our results highlight how the proposed protocol allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, the peptide backbone, and its microenvironment. Full article
(This article belongs to the Section Computational and Theoretical Chemistry)
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17 pages, 1168 KiB  
Article
Analytical Solitary Wave Solutions of Fractional Tzitzéica Equation Using Expansion Approach: Theoretical Insights and Applications
by Wael W. Mohammed, Mst. Munny Khatun, Mohamed S. Algolam, Rabeb Sidaoui and M. Ali Akbar
Fractal Fract. 2025, 9(7), 438; https://doi.org/10.3390/fractalfract9070438 - 3 Jul 2025
Cited by 1 | Viewed by 301
Abstract
In this study, we investigate the fractional Tzitzéica equation, a nonlinear evolution equation known for modeling complex phenomena in various scientific domains such as solid-state physics, crystal dislocation, electromagnetic waves, chemical kinetics, quantum field theory, and nonlinear optics. Using the (G′/ [...] Read more.
In this study, we investigate the fractional Tzitzéica equation, a nonlinear evolution equation known for modeling complex phenomena in various scientific domains such as solid-state physics, crystal dislocation, electromagnetic waves, chemical kinetics, quantum field theory, and nonlinear optics. Using the (G′/G, 1/G)-expansion approach, we derive different categories of exact solutions, like hyperbolic, trigonometric, and rational functions. The beta fractional derivative is used here to generalize the classical idea of the derivative, which preserves important principles. The derived solutions with broader nonlinear wave structures are periodic waves, breathers, peakons, W-shaped solitons, and singular solitons, which enhance our understanding of nonlinear wave dynamics. In relation to these results, the findings are described by showing the solitons’ physical behaviors, their stabilities, and dispersions under fractional parameters in the form of contour plots and 2D and 3D graphs. Comparisons with earlier studies underscore the originality and consistency of the (G′/G, 1/G)-expansion approach in addressing fractional-order evolution equations. It contributes new solutions to analytical problems of fractional nonlinear integrable systems and helps understand the systems’ dynamic behavior in a wider scope of applications. Full article
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