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19 pages, 2844 KiB  
Article
Interaction Mechanisms of KRAS G12C Inhibitors (Sotorasib and Adagrasib) with Human Serum Albumin: Insights from Spectroscopic and Molecular Docking Studies
by Junsong Qin, Zhepeng Chen, Chuangyan Wang, Lin Mai, Xian Wang, Junfeng Li, Hui Liu and Yun Song
Molecules 2025, 30(16), 3436; https://doi.org/10.3390/molecules30163436 - 20 Aug 2025
Abstract
This study systematically explored the interaction mechanisms between two KRAS G12C inhibitors (Sotorasib and Adagrasib) and human serum albumin (HSA) via UV-vis spectroscopy, fluorescence spectroscopy, three-dimensional fluorescence spectroscopy, and molecular docking methods. The experimental findings demonstrated that both drugs caused static quenching of [...] Read more.
This study systematically explored the interaction mechanisms between two KRAS G12C inhibitors (Sotorasib and Adagrasib) and human serum albumin (HSA) via UV-vis spectroscopy, fluorescence spectroscopy, three-dimensional fluorescence spectroscopy, and molecular docking methods. The experimental findings demonstrated that both drugs caused static quenching of HSA fluorescence, with binding constants of 13.64 × 103 M−1 (Sotorasib) and 63.67 × 103 M−1 (Adagrasib), demonstrating significant selectivity differences in their binding affinities. UV spectral analysis demonstrated distinct microenvironmental perturbations: Sotorasib and Adagrasib induced a shift (∆λ = 7 nm and ∆λ = 8 nm, respectively) at 211 nm, consistent with altered polarity in HSA’s binding pockets. Fluorescence spectroscopy confirmed a 1:1 binding stoichiometry, with Stern-Volmer analysis validating static quenching as the dominant mechanism. Three-dimensional fluorescence spectra further highlighted Adagrasib’s stronger conformational impact, reducing tyrosine and tryptophan residue fluorescence intensities by 16% (Peak 1) and 10% (Peak 2), respectively, compared to Sotorasib. Molecular docking revealed divergent binding modes: Sotorasib occupied Sudlow Site I via three hydrogen bonds and hydrophobic interactions (∆G = −24.60 kJ·mol−1), whereas Adagrasib bound through one hydrogen bond and hydrophobic forces (∆G = −30.92 kJ·mol−1), with stability differences attributed to structural characteristics. This study uses multispectral technology and molecular docking to reveal the binding mechanism of Sotorasib and Adagrasib with HSA, providing a theoretical basis for designing highly targeted albumin nanocarriers. The strong binding properties of Adagrasib and HSA may reduce the toxicity of free drugs, providing direction for the development of long-acting formulations. Full article
20 pages, 3014 KiB  
Article
Investigation of the Effect of NaCl Concentrations on the Formation of Amyloid Fibrils During the Cooking of Wheat Noodles
by Ying Liang, Chunlei Zheng, Liu Yang, Minqian Huang, Jiajia Liu, Hao Liu, Baoshan He and Jinshui Wang
Foods 2025, 14(16), 2892; https://doi.org/10.3390/foods14162892 - 20 Aug 2025
Abstract
In our previous study, we observed that sodium chloride (NaCl) influences the formation of amyloid fibrils (AFs) by gluten in cooked wheat noodles. However, the underlying mechanisms of NaCl’s effect on AF formation during the cooking process remain unclear. This study systematically investigates [...] Read more.
In our previous study, we observed that sodium chloride (NaCl) influences the formation of amyloid fibrils (AFs) by gluten in cooked wheat noodles. However, the underlying mechanisms of NaCl’s effect on AF formation during the cooking process remain unclear. This study systematically investigates the impact of NaCl concentration (0–2.0%, w/w) and cooking time (0–7 min) on AF formation. ThT fluorescence and Congo red confirmed AF formation across all NaCl concentration levels. At low NaCl concentrations, Na+/Cl shielding reduced electrostatic repulsion, enabling ordered β-sheet stacking, yielding long fibrils (1193 nm) with high β-sheet content (41.5%), dense cross-β structures, and elevated hydrophobicity (H0 = 9980). Stable zeta potential and gradual particle growth (376 to 1193 nm) supported controlled elongation. Conversely, high NaCl concentrations disrupted hydrogen bonding, forming shorter fibrils (820 nm) with reduced β-sheets (28.9%) and lower hydrophobicity (H0 = 5923). Rapid ThT kinetics (df/dt = 77,535 FU/min) and SE-HPLC profiles suggest that elevated concentrations of NaCl inhibit AF formation while inducing the generation of amorphous aggregates. These findings clarify the balance between ionic shielding and hydrophobic interactions in AF assembly, offering strategies to optimize noodle texture. Future studies should address the digestibility and health implications of salt-modulated AFs for functional food applications. Full article
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24 pages, 4005 KiB  
Article
Separation of the Biofuel Methyl Ethyl Ketone from Aqueous Solutions Using Avocado-Based Activated Carbons: Synthesis Conditions and Multilayer Adsorption Properties
by Hilda Elizabeth Reynel-Avila, Eduardo Ledea-Figueredo, Lizbeth Liliana Díaz-Muñoz, Adrián Bonilla-Petriciolet, Ismael Alejandro Aguayo-Villarreal, Laura Gabriela Elvir-Padilla and Carlos Javier Durán-Valle
Molecules 2025, 30(16), 3426; https://doi.org/10.3390/molecules30163426 - 20 Aug 2025
Abstract
This study reports the separation of methyl ethyl ketone (MEK), a relevant compound in the biorefinery context, from aqueous solutions using activated carbons derived from avocado seed biomass. Two synthesis routes were explored via chemical and thermal activation with H2SO4 [...] Read more.
This study reports the separation of methyl ethyl ketone (MEK), a relevant compound in the biorefinery context, from aqueous solutions using activated carbons derived from avocado seed biomass. Two synthesis routes were explored via chemical and thermal activation with H2SO4 and KOH. A Taguchi experimental design was applied to tailor synthesis conditions, with MEK adsorption capacity as the target property. Adsorption kinetics and isotherms were evaluated to determine the thermodynamic behavior of MEK separation using the best-performing activated carbons. The carbon activated with H2SO4 achieved the highest adsorption capacity (142 mg g−1) at 20 °C and pH 4, surpassing KOH-based materials. This enhanced performance correlated to increased surface area and acidic oxygenated functionalities. However, higher pH and temperature reduced the adsorption efficiency for all adsorbents. Comprehensive characterization was performed using XRD, XRF, FTIR, SEM, N2 adsorption–desorption isotherms, pH at point of zero charge, and surface acidity/basicity analysis via Boehm titration. Thermodynamic data and surface characterization indicated that MEK adsorption occurs via a double-layer mechanism dominated by electrostatic interactions and hydrogen bonding. The findings highlight an optimized approach for tailoring avocado-based activated carbons to efficiently recover MEK from aqueous media, supporting its potential application in downstream purification of fermentation broths for biofuel production and energy transition processes. Full article
(This article belongs to the Special Issue Porous Carbon Materials: Preparation and Application)
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13 pages, 2635 KiB  
Article
Structure and Nonlinear Optical Characterization of a New Acentric Crystal of a 4-Hydroxybenzohydrazide Derivative
by Emanuela Santagata, Yovan de Coene, Stijn Van Cleuvenbergen, Koen Clays, Emmanuele Parisi, Fabio Borbone and Roberto Centore
Crystals 2025, 15(8), 739; https://doi.org/10.3390/cryst15080739 (registering DOI) - 20 Aug 2025
Abstract
We report the crystal structure and nonlinear optical (NLO) characterization of the monohydrate form of N′-[(E)-(2-fluorophenyl)methylidene]-4-hydroxybenzohydrazide (o-FHH), an organic compound showing strong potential for second-order nonlinear optical applications. The compound crystallizes in a non-centrosymmetric tetragonal space group. The supramolecular features of [...] Read more.
We report the crystal structure and nonlinear optical (NLO) characterization of the monohydrate form of N′-[(E)-(2-fluorophenyl)methylidene]-4-hydroxybenzohydrazide (o-FHH), an organic compound showing strong potential for second-order nonlinear optical applications. The compound crystallizes in a non-centrosymmetric tetragonal space group. The supramolecular features of the novel crystal structure are strongly related to the role of the water molecule that stabilized columns of o-FHH through strong hydrogen bonding interactions. This structural feature is reflected in the high thermal stability of the compound, which is evidenced by its ability to withstand temperatures in excess of 100 °C without losing the water molecule. Second-harmonic generation (SHG) imaging confirms bulk nonlinearity throughout the entire volume of the crystal, consistent with the acentric class of the novel compound. The combination of a dense hydrogen-bonding network, structural robustness, and the ability to grow millimeter-sized single crystals makes o-FHH a good candidate for further development as an organic NLO material. Full article
(This article belongs to the Section Organic Crystalline Materials)
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14 pages, 3021 KiB  
Article
Formation of Supramolecular Structures in Oxidation Processes Catalyzed by Heteroligand Complexes of Iron and Nickel: Models of Enzymes
by Ludmila Ivanovna Matienko, Elena M. Mil, Anastasia A. Albantova and Alexander N. Goloshchapov
Int. J. Mol. Sci. 2025, 26(16), 8024; https://doi.org/10.3390/ijms26168024 - 19 Aug 2025
Abstract
In some cases, the catalytic processes involve the formation of self-organized supramolecular structures due to H-bonds and other non-covalent interactions. It has been suggested that the construction of self-assembled catalytic systems is a promising strategy to mimic enzyme catalysis at the model level. [...] Read more.
In some cases, the catalytic processes involve the formation of self-organized supramolecular structures due to H-bonds and other non-covalent interactions. It has been suggested that the construction of self-assembled catalytic systems is a promising strategy to mimic enzyme catalysis at the model level. As a rule, the real catalysts are not the primary catalytic complexes, but rather, those that are formed during the catalytic process. In our earlier works, we have established that the effective catalysts M(II)xL1y(L1ox)z(L2)n(H2O)m (M = Ni, Fe, L1 = acac, L2 = activating electron-donating ligand) for the selective oxidation of ethylbenzene to α-phenyl ethyl hydroperoxide are the result of the transformation of primary (Ni(Fe)L1)x(L2)y complexes during the oxidation of ethylbenzene. In addition, the mechanism of the transformation to active complexes is similar to the mechanism of action of NiFeARD (NiFe-acireductone dioxygenase). Based on kinetic and spectrophotometric data, we hypothesized that the high stability of effective catalytically active complexes may be associated with the formation of stable supramolecular structures due to intermolecular hydrogen bonds and possibly other non-covalent bonds. We confirmed this assumption using AFM. In this work, using AFM, we studied the possibility of forming supramolecular structures based on iron complexes with L2-crown ethers and quaternary ammonium salts, which are catalysts for the oxidation of ethylbenzene and are models of FeARD (Fe-acireductone dioxygenase). The formation of supramolecular structures based on complexes of natural Hemin with PhOH and L-histidine or Hemin with L-tyrosine and L-histidine, which are models of heme-dependent tyrosine hydroxylase and cytochrome P450-dependent monooxygenases (AFM method), may indicate the importance of outer-sphere regulatory interactions with the participation of Tyrosine and Histidine in the mechanism of action of these enzymes. Full article
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38 pages, 6660 KiB  
Review
Field-Effect Crystal Engineering in Proton–π-Electron Correlated Systems
by Sachio Horiuchi, Hiromi Minemawari, Jun’ya Tsutsumi and Shoji Ishibashi
Crystals 2025, 15(8), 736; https://doi.org/10.3390/cryst15080736 - 19 Aug 2025
Abstract
Dielectric crystals with switchable electric polarizations represent the key functional materials utilized for a broad range of practical applications. They allow for academically intriguing platforms, where the use of a strong external electric field can potentially unveil hidden crystal phases. Proton–π-electron correlated bistable [...] Read more.
Dielectric crystals with switchable electric polarizations represent the key functional materials utilized for a broad range of practical applications. They allow for academically intriguing platforms, where the use of a strong external electric field can potentially unveil hidden crystal phases. Proton–π-electron correlated bistable systems turn out to be promising for exploring such electrically induced crystal polymorphisms, mainly because strong π-electronic polarization can be sensitively switched depending on mobile hydrogen locations. Pseudo-symmetry and hydrogen disorder are utilized as clues for the data mining of the Cambridge Structural Database in the search for molecular candidates with novel switchable dielectrics. The polarization hysteresis, electrostriction, and second harmonic generation of the candidates were experimentally evaluated, together with the re-inspection of crystal structure. This feature article highlights the rich variation and competition of some candidate polarization configurations and switching modes in close relation to high and efficient electrical energy storage/discharge, large electrostriction effects, polarization rotations, and multistage switching phenomena. The experimental findings are well-reproduced by the computational optimization of crystal structure and the simulation of the switchable polarization, piezoelectric coefficients, and relative stability for each of the real or hypothetical hydrogen-ordered crystal phases. Effective prediction and strategic design are thereby guaranteed by systematically understanding the appropriate integration of experimental, computational, and data sciences. Full article
(This article belongs to the Special Issue Polymorphism and Phase Transitions in Crystal Materials)
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13 pages, 4494 KiB  
Article
Molecular Dynamics Simulation Analysis of JAK1 Initial Activation: Phosphorylation-Induced Conformational Dynamics and Domain Interactions
by Xinyu Peng, Kefu Liu, Guodong Chen and Shengjie Sun
Life 2025, 15(8), 1316; https://doi.org/10.3390/life15081316 - 19 Aug 2025
Abstract
Janus kinase is critical for cytokine-mediated signaling, and its hyperactivation due to mutations drives various diseases. The activation of Janus kinase 1 (JAK1) involves a conformational transition from a closed to an open state, but the underlying mechanism remains unclear. This study investigates [...] Read more.
Janus kinase is critical for cytokine-mediated signaling, and its hyperactivation due to mutations drives various diseases. The activation of Janus kinase 1 (JAK1) involves a conformational transition from a closed to an open state, but the underlying mechanism remains unclear. This study investigates the roles of two tyrosine residues, Y1034 and Y1035, within the activation loop of the tyrosine kinase domain. Molecular dynamics simulations reveal that phosphorylation, particularly bisphosphorylation at Y1034 and Y1035, promotes the transition to the open conformation, with pY1035 exerting a greater influence than pY1034. Phosphorylation increases the negative charge on the TK domain surface, facilitating its dissociation from the FERM domain, while also weakening TK-FERM interactions. However, the loop between the TK and PK domains formed stable hydrogen bonds with other domains, hindering the full activation process. Using 1 µs molecular dynamics simulations is not sufficient for full activation. These findings elucidate the molecular mechanisms governing the JAK1 initial activation and provide insights for targeting its regulation in disease contexts. Full article
(This article belongs to the Section Biochemistry, Biophysics and Computational Biology)
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14 pages, 5789 KiB  
Article
Investigation of the Influence of Pyrolysis Temperature on the Adsorption Performance of Municipal Sludge-Derived Biochar Toward Metal Ions
by Xiaomin Yang, Quanfeng Wang, Yuanling Cheng, Long Qin, Yan Zhao, Yanglu Tang and Da Sun
Water 2025, 17(16), 2459; https://doi.org/10.3390/w17162459 - 19 Aug 2025
Abstract
In response to the growing issue of iron and manganese pollution in water bodies, this study systematically investigated the adsorption performance of municipal sludge-derived biochar prepared at pyrolysis temperatures ranging from 300 to 700 °C for the removal of Fe2+ and Mn [...] Read more.
In response to the growing issue of iron and manganese pollution in water bodies, this study systematically investigated the adsorption performance of municipal sludge-derived biochar prepared at pyrolysis temperatures ranging from 300 to 700 °C for the removal of Fe2+ and Mn2+. Among the series of adsorbents (BC300–BC700), BC600—with its well-developed pore structure and high specific surface area—exhibited the best adsorption performance for both metal ions. Kinetic and isothermal adsorption experiments, in combination with XPS characterization, collectively revealed that (1) the adsorption mechanisms of Fe and Mn differ markedly, with Fe adsorption primarily governed by physical interactions, whereas Mn adsorption is largely controlled by chemical processes; (2) Fe2+ adsorption occurs mainly via electrostatic interactions and hydrogen bonding; and (3) Mn2+ forms carbonate precipitates with C=O groups during redox reactions. Thermodynamic analysis further indicated that the adsorption process was spontaneous and endothermic. Moreover, BC600 demonstrated excellent reusability for Fe adsorption across different water matrices, maintaining efficiencies above 95% after five cycles, although the adsorption performance for Mn declined. This study provides theoretical support for the application of sludge-derived biochar as a cost-effective and efficient adsorbent for metal ion remediation. Full article
(This article belongs to the Special Issue Water Pollution Control and Ecological Restoration: 2nd Edition)
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35 pages, 3721 KiB  
Review
Research Progress of Supramolecular Gels in the Field of Petroleum Engineering
by Liyao Dai, Jinsheng Sun, Kaihe Lv, Yingrui Bai, Jianlong Wang, Chaozheng Liu and Mei-Chun Li
Gels 2025, 11(8), 661; https://doi.org/10.3390/gels11080661 - 19 Aug 2025
Abstract
Traditional petroleum engineering materials have problems such as single functionality and poor environmental adaptability in terms of lost circulation control and enhanced oil recovery. Supramolecular gels, with their dynamic reversible non-covalent network structure, demonstrate unique advantages in this regard. This paper classifies supramolecular [...] Read more.
Traditional petroleum engineering materials have problems such as single functionality and poor environmental adaptability in terms of lost circulation control and enhanced oil recovery. Supramolecular gels, with their dynamic reversible non-covalent network structure, demonstrate unique advantages in this regard. This paper classifies supramolecular gels into hydrogen bond type, metal coordination type, host–guest type, and electrostatic interaction type based on differences in crosslinking structures. It explains the construction principles and characteristics of each type of gel and analyses their application progress in petroleum engineering fields, such as lost circulation control in drilling, temporary plugging in fracturing, and profile control in enhanced oil recovery. It also discusses the advantages and disadvantages of different systems and future development directions. Research has shown that the molecular design strategy of supramolecular gels can effectively address technical challenges under complex conditions, offering new insights for oil and gas field development. Further optimization of their long-term stability and large-scale production technology is needed to advance their practical application. Full article
(This article belongs to the Special Issue Polymer Gels for the Oil and Gas Industry)
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29 pages, 3388 KiB  
Article
A Dual-Template Molecularly Imprinted Polymer to Inhibit Quorum Sensing Molecules: Theoretical Design, Optimized Synthesis, Physicochemical Characterization and Preliminary Microbiological Analysis
by Khonzisizwe Somandi, Tama S. Mwale, Monika Sobiech, Dorota Klejn, Gillian D. Mahumane, Joanna Giebułtowicz, Sandy van Vuuren, Yahya E. Choonara and Piotr Luliński
Int. J. Mol. Sci. 2025, 26(16), 8015; https://doi.org/10.3390/ijms26168015 - 19 Aug 2025
Abstract
Molecularly imprinted polymers (MIPs) have emerged as promising materials for selectively targeting biomolecules, including quorum sensing autoinducers that regulate bacterial communication and biofilm formation. In this study, both single-template and dual-template strategies were employed to design and synthesize MIPs capable of capturing autoinducer-2 [...] Read more.
Molecularly imprinted polymers (MIPs) have emerged as promising materials for selectively targeting biomolecules, including quorum sensing autoinducers that regulate bacterial communication and biofilm formation. In this study, both single-template and dual-template strategies were employed to design and synthesize MIPs capable of capturing autoinducer-2 analogs using (3R,4S)-tetrahydro-3,4-furandiol (T1) or (R/S) 2,2-dimethyl-1,3-dioxolane-4-methanol (T2) as the templates. This approach offers translational potential of a complementary or non-antibiotic strategy to conventional antimicrobial therapies in mitigating biofilm-associated infections. Computational modeling guided the rational selection of functional monomers, predicting favorable interaction energies (ΔEC up to −135 kcal·mol−1) and optimal hydrogen-bonding patterns to enhance template–polymer affinity. The synthesized MIPs were characterized using spectroscopic and microscopic techniques to confirm imprinting efficiency and structural integrity. The adsorption capacity measurements demonstrated higher adsorption capacity and selectivity of MIPs compared to non-imprinted polymers, with the highest selectivity equal to 3.36 for T1 and 3.14 for T2 on MIPs fabricated from methacrylic acid. Preliminary microbiological evaluations using Chromobacterium violaceum ATCC 12472 reveal that the MIPs prepared from 2-hydroxyethyl methacrylate effectively inhibited violacein production by up to 78.2% at 5.0 mg·mL−1, consistent with quorum sensing interference. These findings highlight the feasibility of employing molecular imprinting to target autoinducer-2 analogs, introducing a novel synthetic strategy for disrupting bacterial communication. This further suggests that molecular imprinting can be leveraged to develop potent quorum-sensing inhibitors, an approach that offers translational potential as an alternative to conventional antimicrobial strategies to mitigate biofilm-associated infections. Full article
(This article belongs to the Section Materials Science)
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12 pages, 2329 KiB  
Article
Comparative Analysis of the Substituent Effects on the Supramolecular Structure of N′-(4-Methyl-2-nitrophenyl)benzohydrazide and N′-(2-Nitro-(4-trifluoromethyl)phenyl)benzohydrazide)
by Christos P. Constantinides, Syed Raza, Fadwat Bazzi, Nisreen Sharara and Simona Marincean
Crystals 2025, 15(8), 732; https://doi.org/10.3390/cryst15080732 - 19 Aug 2025
Abstract
N′-Phenylbenzohydrazides are valuable precursors for air- and moisture-stable Blatter radicals, with applications in magnetism and spintronics. This study presents the single-crystal X-ray structures of N′-(4-methyl-2-nitrophenyl)benzohydrazide (I) and N′-(2-nitro-(4-trifluoromethyl)phenyl)benzohydrazide (II), highlighting the influence of substituents on supramolecular [...] Read more.
N′-Phenylbenzohydrazides are valuable precursors for air- and moisture-stable Blatter radicals, with applications in magnetism and spintronics. This study presents the single-crystal X-ray structures of N′-(4-methyl-2-nitrophenyl)benzohydrazide (I) and N′-(2-nitro-(4-trifluoromethyl)phenyl)benzohydrazide (II), highlighting the influence of substituents on supramolecular arrangement. Compounds I and II are found to crystallize within the monoclinic crystal system, with the space groups I2/a and P21/n, respectively, with centrosymmetric, one-dimensional columnar packing driven by π-π stacking. In I, π-π dimers form between benzoyl rings (3.018 Å), with additional stacking between aryls (3.408 Å) of neighboring dimers. In II, alternating benzoyl and aryl rings stack with interplanar distances of 2.681 and 2.713 Å. Bifurcated intra- and intermolecular hydrogen bonds (1.938–2.478 Å) further stabilize the packing. Compound II exhibits inter-stack F···F contacts (2.924 Å), attributed to steric effects. The trifluoromethyl group enhances N′NCO-NO2 conjugation, resulting in a near-parallel arrangement of aromatic rings and planar geometry at the N′ nitrogen. In contrast, compound I shows reduced conjugation, leading to pyramidalization at the N′ nitrogen and increased hydrazide bond flexibility, as seen in the 56° angle between aromatic rings. Full article
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18 pages, 2600 KiB  
Article
Scandium(III) Solvation and Association and Water Structure in the Gigapascal Pressure Range Investigated by Neutron Scattering
by Toshio Yamaguchi, Sinichi Machida and Takanori Hattori
Molecules 2025, 30(16), 3417; https://doi.org/10.3390/molecules30163417 - 19 Aug 2025
Abstract
Scandium(III) (Sc(III)) is the smallest among the trivalent ions in Group 3, which includes yttrium(III) and lanthanides (III) with a hydration number of 8 and 8–9, respectively. The hydration number of Sc(III) in aqueous solutions reported so far varies from six to ten [...] Read more.
Scandium(III) (Sc(III)) is the smallest among the trivalent ions in Group 3, which includes yttrium(III) and lanthanides (III) with a hydration number of 8 and 8–9, respectively. The hydration number of Sc(III) in aqueous solutions reported so far varies from six to ten and remains an open question. In general, applying pressure and temperature to aqueous solutions perturbs the water structure and ion solvation, providing insight into the nature of ion solvation. In the present study, we perform neutron scattering measurements of a 1 m (mol/kg) ScCl3 aqueous solution in D2O (hereafter H is used to symbolize the hydrogen atom instead of D) under the thermodynamic conditions from 0.1 MPa/298 K to 4 GPa/523 K. Using the empirical potential structure refinement (EPSR) method, the neutron scattering data are analyzed to extract the site–site pair distribution functions, coordination number distributions, angle distributions, and spatial density functions (3D structure). A predominant Sc(III) species is [Sc(OH2)7]3+ with a distorted pentagonal bipyramidal geometry together with appreciable amounts of contact ion pair species [ScCln(OH2)(6−n)](3−n)+ (n = 1–3) and [Sc(OH2)8]3+ with mean Sc–Cl and Sc–OH2 distances of 2.42 and 2.11 Å, respectively. An aqua chloride ion is surrounded on average by 7.8 and 10.9 water molecules with a Cl–H2O distance of 3.10 Å at 0.1 MPa/298 K and 4 GPa/523 K, respectively. Applying GPa pressure transforms the tetrahedral network structure of water under ambient conditions to a dense, randomly packed structure with a mean coordination number of 12.6, resulting in an increase in the first-neighbor distance from 2.77 to 2.89 Å. The hydrogen bonds between water molecules remain linear but are largely distorted at high temperatures and high pressures. The present results provide a hint for understanding the underlying mechanism of high-pressure and temperature coordination chemistry and in applied fields, such as processes in geochemistry of the Earth’s upper mantle and pressure-induced protein denaturation. Full article
(This article belongs to the Special Issue Influence of Solvent Molecules in Coordination Chemistry)
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20 pages, 2572 KiB  
Article
Ball-Milling-Assisted Fe3O4 Loadings of Rice Straw Biochar for Enhanced Tetracycline Adsorption in Aquatic Systems
by Yuxin Liu, Haizhang Yu, Yuchen Xing, Qi Zhao, Rukeya Ashan, Bo Feng, Bo Tao, Qianyi Shangguan, Yucheng Liu, Haiyan Zhang and Guanya Ji
Agronomy 2025, 15(8), 1987; https://doi.org/10.3390/agronomy15081987 - 19 Aug 2025
Abstract
Antibiotic contaminants such as tetracycline (TC) from agricultural production have become widely distributed and persistently accumulated in aquatic environments (rivers, lakes, and oceans), posing severe threats to ecological security and human health. This study developed a modified rice-straw-derived biochar through NaOH activation and [...] Read more.
Antibiotic contaminants such as tetracycline (TC) from agricultural production have become widely distributed and persistently accumulated in aquatic environments (rivers, lakes, and oceans), posing severe threats to ecological security and human health. This study developed a modified rice-straw-derived biochar through NaOH activation and ball-milling-assisted Fe3O4 loading, which simultaneously enhanced TC adsorption capacity and enabled magnetic recovery. The Box–Behnken design (BBD) response surface methodology was employed to optimize three key preparation parameters: ball-milling time (A, 39.95 min), frequency (B, 57.23 Hz), and Fe3O4/biochar mass ratio (C, 2.85:1), with TC adsorption capacity as the response value. The modified biochar was systematically characterized using SEM, BET, FTIR, XRD, and XPS, while adsorption mechanisms were elucidated through kinetic studies, isotherm analyses, and pH-dependent experiments. The results demonstrate that modification via ball-milling with Fe3O4 loading significantly enhanced the biochar’s tetracycline adsorption capacity. The maximum adsorption capacity of the modified biochar reached 102.875 mg/g, representing a 114.85% increase from the initial value of 47.882 mg/g observed for the pristine biochar. Furthermore, the modified biochar exhibited excellent stability, maintaining robust adsorption performance across a wide pH range. The primary adsorption mechanisms involved metal coordination complexation, supplemented by hydrogen bonding, π-π interactions, and pore filling. Full article
(This article belongs to the Section Agricultural Biosystem and Biological Engineering)
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16 pages, 10427 KiB  
Article
Comparative Analysis of Structural Characterisation and Gel Properties of Blended/Co-Precipitated Soy-Pea Dual-Protein
by Lu Wang, Xinyu Zhang, Xinhui Wang, Aiting Hui, Fengying Xie and Xia Wu
Foods 2025, 14(16), 2867; https://doi.org/10.3390/foods14162867 - 19 Aug 2025
Abstract
This study proposed a pH-driven co-precipitation strategy to overcome the limitations of traditional physical blending in functional improvement of a dual-protein system. The results demonstrated that, in comparison with the soy-pea blended protein (SPBP), the soy-pea co-precipitated protein (SPCP) showed a decrease in [...] Read more.
This study proposed a pH-driven co-precipitation strategy to overcome the limitations of traditional physical blending in functional improvement of a dual-protein system. The results demonstrated that, in comparison with the soy-pea blended protein (SPBP), the soy-pea co-precipitated protein (SPCP) showed a decrease in α-helix and β-sheet content, accompanied by in an increase in random coil structure. SPCP exhibited decreased fluorescence intensity, smaller particle size (from 392.2 to 176.1 nm) with increased absolute zeta-potential values (from −13.7 to −19.7 mV), reduced surface hydrophobicity (from 21,987.3 to 9744.8), and increased content of disulfide bonds. Structural optimization of SPCP significantly bolstered intermolecular interactions between SPI and PPI. Molecular docking simulations also validated the presence of abundant hydrophobic interactions and hydrogen bonds within in the blend system. These modifications significantly enhanced the solubility of SPCP (especially SPCP8.0). The rheological analysis further revealed that the storage modulus (G′) and loss modulus (G″) of SPCP8.0 were both higher than those of SPBP, while its tan δ was lower than that of SPBP, indicating synergistic interactions between proteins. These interactions contributed to the formation of a more stable three-dimensional network structure, thereby conferring it with superior gel properties. These findings provide theoretical foundations for improving the functional properties of plant-based dual-protein and their applications in plant-based meat production. Full article
(This article belongs to the Special Issue Advances in the Development of Proteins from Grains and Legumes)
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12 pages, 4939 KiB  
Article
Engineering Malic Enzyme CO2 Fixation Activity via a Structure–Sequence–SCANNER (3S) Co-Evolution Strategy
by Jianping Shi, Mingdong Wang, Ting Feng, Xianglong Li, Yanbin Feng and Song Xue
Catalysts 2025, 15(8), 789; https://doi.org/10.3390/catal15080789 - 18 Aug 2025
Abstract
Enzymatic CO2 fixation offers great potential for the sustainable synthesis of value-added compounds. Malic enzyme (ME) catalyzes the reverse carboxylation of pyruvate to malate, enabling direct CO2 conversion into C4 compounds with broad biosynthetic applications. However, the reverse carboxylation activity [...] Read more.
Enzymatic CO2 fixation offers great potential for the sustainable synthesis of value-added compounds. Malic enzyme (ME) catalyzes the reverse carboxylation of pyruvate to malate, enabling direct CO2 conversion into C4 compounds with broad biosynthetic applications. However, the reverse carboxylation activity of wild-type ME is insufficient, and conventional enzyme engineering strategies remain limited by the complexity of identifying distal functional sites. Here, we present a Structure–Sequence–SCANNER (3S) co-evolution strategy that integrates protein structural analysis, sequence conservation profiling, and co-evolutionary network analysis to enable systematic identification of functionally relevant hotspot residues. Using this approach, we engineered Escherichia coli ME (EcME) variants with enhanced CO2 fixation activities. In total, 106 single-point variants were constructed and screened. Among these, variants A464S and D97E exhibited significantly improved reverse carboxylation activities, with 1.7-fold and 1.6-fold increases in catalytic activity and 1.5-fold and 1.8-fold improvements in catalytic efficiency (kcat/Km), respectively, compared to wild-type EcME. Their catalytic efficiencies (kcat/Km) improved by 1.5-fold and 1.8-fold, increasing from 80 mM−1·min−1 for the wild-type enzyme to 120 and 130 mM−1·min−1, respectively. Mechanistic analyses revealed that A464S introduces a stabilizing hydrogen bond with N462, enhancing NADPH binding, while D97E forms a new salt bridge network with K513, resulting in contraction of the substrate pocket entrance and increased pyruvate affinity. These findings demonstrate the effectiveness of the 3S strategy in reprogramming enzyme functions and highlight its potential for constructing efficient artificial CO2 fixation systems. Full article
(This article belongs to the Section Biocatalysis)
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