Search Results (258)

The retention of polyphenols in thermally processed noodles is constrained by interactions with starch and glutenin, critically impacting functional properties (antioxidant activity, starch digestibility modulation) and quality attributes. Current understanding lacks quantitative links between initial pomace particle size, polyphenol behavior throughout processing, and the resulting noodle properties. This study systematically investigated how Rosa roxburghii pomace particle size (0.1–250 μm), fractionated into five ranges, governs polyphenol extractability, retention in fresh/boiled noodles, and their functional and quality outcomes. Mathematical modeling established quantitative particle size–property relationships. The results indicated that polyphenol release was maximized at the 1–10 μm particle size. Total phenolic retention in boiled noodles was highest with 0.1–1 μm pomace, while the retention of specific phenolics peaked with 60–80 μm pomace. Fresh noodle hardness and gumminess decreased significantly, particularly with extracts from 1 to 40 μm pomace, whereas boiled noodles showed increased chewiness/adhesiveness. All polyphenol-enriched noodles exhibited suppressed starch digestibility and enhanced antioxidant capacity. Robust quadratic regression models predicted key properties based on particle size. Molecular interactions (hydrogen bonding, hydrophobic contacts, π–cation stacking, salt bridges) between key phenolics (EGCG, hydroxybenzoic acid, gallic acid, quercetin, and isoquercitrin) and the gluten–starch matrix, critically involving residues Arg-86 and Arg-649, were identified as the underlying mechanism. These results demonstrate that precise control of pomace particle size regulates extract composition and molecular binding dynamics, providing a strategic approach to optimize functional noodle design. Full article

We have theoretically examined the intermolecular interactions in the cationic states of π-stacked dimers of 4nπ antiaromatic molecules. The ground state of face-to-face π-dimer models, consisting of cyclobutadienes (CBDs), was analyzed as a function of the stacking distance (d) for their monocationic and dicationic states using multi-reference second-order perturbation theory. Multi-configurational wavefunction analysis in a diabatic representation was employed to understand the electronic structures of the dimer models in terms of the monomer electron configurations. It is found that the monocationic dimer exhibits a local minimum at about d = 2.4 Å in the ground state, where each monomer is represented by a superposition between neutral triplet and cationic doublet electron configurations. Crossing of the ground and excited states occurs through changing d, which is due to the small energy gap between the highest occupied and lowest unoccupied molecular orbitals of antiaromatic molecules. Full article

Background: TRPC6 is recognized as a therapeutically relevant cation channel, whose activation is governed by specific ligand–pocket interactions. Methods: An integrated in silico workflow was employed, comprising structure-based docking, 100-nanosecond molecular dynamics (MD) simulations, and MM-GBSA calculations. Benzoic-acid–based compounds were designed and prioritized for binding to the TRPC6 pocket, using a known literature agonist as a reference for benchmarking. Results: Within the compound series, BT11 was found to exhibit a representative interaction profile, characterized by a key hydrogen bond with Trp680 (~64% occupancy), persistent salt-bridge interactions with Lys676 and Lys698, and π–π stacking with Phe675 and Phe679. A favorable docking score (−11.45 kcal/mol) was obtained for BT11, along with a lower complex RMSD during MD simulations (0.6–4.8 Å), compared with the reference compound (0.8–7.2 Å). A reduction in solvent-accessible surface area (SASA) after ~60 ns was also observed, suggesting decreased water penetration. The most favorable binding energy was predicted for BT11 by MM-GBSA (−67.72 kcal/mol), while SOH95 also ranked highly and slightly outperformed the reference. Conclusions: These convergent computational analyses support the identification of benzoic-acid–derived chemotypes as potential TRPC6 ligands. Testable hypotheses are proposed, along with structure–activity relationship (SAR) guidelines, to inform experimental validation and guide the design of next-generation analogs. Full article

This study aimed to develop an environmentally friendly and relatively efficient method for extracting natural antioxidants from avocado by-products while investigating the antioxidant mechanisms of their core bioactive components on multiple dimensions. In vitro antioxidant assays (ABTS, FRAP, SAFR, SFR, ORAC, DPPH) demonstrated that flavonoid procyanidin was the primary antioxidant component in avocado seeds, exhibiting the strongest activity (DPPH EC₅₀ = 3.6 µg/mL). The Hill model indicated a positive synergistic effect (n = 3.1). Chemical and molecular mechanism analyses revealed that avocado seeds exert antioxidant activity predominantly through hydrogen atom transfer (HAT) and electron transfer (ET) pathways. The model predictions suggested procyanidins may stably bind to protein targets in the Keap1-Nrf2 pathway and NOX2 via hydrogen bonding, hydrophobic interactions, and π-cation interactions. Furthermore, response surface methodology (RSM) was employed to optimize the extraction process of avocado seed antioxidants in an ethanol-water system. This study underscores the considerable health benefits and antioxidant capacity of avocado by-products, supporting their promising application in functional foods formulations. Full article

In this study, four types of Fe₃O₄-based magnetic nanospheres were functionalized with distinct surface groups to examine how surface chemistry influences their co-transport with tetracycline (TC) in porous media. The functional groups investigated are carboxyl (−COOH), epoxy (−EPOXY), silanol (−SiOH), and amino (−NH₂). Particles bearing −COOH, −EPOXY, or −SiOH are negatively charged, facilitating their transport through porous media, whereas −NH₂-modified particles acquire a positive charge, leading to strong electrostatic attraction to the negatively charged TC and quartz sand, and consequently substantial retention with reduced mobility. Adsorption of TC onto Fe₃O₄-MNPs is predominantly chemisorptive, driven by ligand exchange and the formation of coordination complexes between the ionizable carboxyl and amino groups of TC and the surface hydroxyls of Fe₃O₄-MNPs. Additional contributions arise from electrostatic interactions, hydrogen bonding, hydrophobic effects, and cation–π interactions. Moreover, the carboxylate moiety of TC can coordinate to surface Fe centers via its oxygen atoms. Molecular dynamics simulations reveal a hierarchy of adsorption energies for TC on the differently modified surfaces: Fe₃O₄-NH₂ > Fe₃O₄-EPOXY > Fe₃O₄-COOH > Fe₃O₄-SiOH, consistent with experimental findings. The results underscore that tailoring the surface properties of engineered nanoparticles substantially modulates their environmental fate and interactions, offering insights into the potential ecological risks associated with these nanomaterials. Full article

A series of novel guanidino-aryl (GA) compounds containing phenanthrene, fluoranthene, fluorene, and naphthalene aromatic cores were synthesized to investigate their interactions with DNA, RNA, and G-quadruplex structures. Among the novel compounds, the phenanthrene-guanidino compound demonstrated the highest micromolar affinity for AT-DNA, possibly due to partial phenanthrene intercalation in addition to hydrogen bonding and electrostatic interactions of guanidine cation. All new guanidino-aryl GA compounds bind strongly to the Tel22 G-quadruplex structure with similar affinities regardless of aromatic core size. The 1:1 stoichiometric complex is stabilised by π-π stacking interactions with the top or bottom G-tetrad, together with strong electrostatic interactions of the guanidino cation. The guanidino-porphyrin PoGU displayed distinct binding stoichiometry, indicating possible sandwiching between two G-quadruplex structures. Within the GA compounds tested, guanidino-fluorene exhibited moderate antimetabolic activity against the HeLa cell line, without selectivity against the healthy cell line. Full article

A novel series of multifunctional tacrine–quinoline hybrids were designed, synthesized, and evaluated as potential anti-Alzheimer’s agents. These compounds incorporate tacrine for cholinesterase’s inhibition and 8-hydroxyquinoline for metal chelation. Piperazine was selected as a linker to provide conformational flexibility and to create favorable cation–π interactions with residues in the mid-gorge region of AChE, enhancing dual-site binding with AChE to inhibit Aβ aggregation. In vitro studies demonstrated submicromolar inhibitory activity toward both AChE and BuChE, particularly for compounds 16e (IC₅₀ = 0.10 μM for AChE, 0.043 μM for BuChE) and 16h (IC₅₀ = 0.21 μM for AChE, 0.10 μM for BuChE). These compounds also exhibited potent inhibition of self-induced Aβ_1–42 aggregation (16e: 80.5% ± 4.4%, 16h: 93.2% ± 3.9% at 20 μM). Kinetic analyses revealed mixed-type inhibition, suggesting dual binding to both CAS and PAS of AChE. UV–vis spectrometry confirmed the chelation of Cu²⁺ and Zn²⁺ ions by the 8-hydroxyquinoline moiety. These findings highlight the tacrine–quinoline scaffold as a promising platform for the discovery of a multitarget-directed anti-AD drug. Full article

With the recent development of accurate protein structure prediction tools, virtually all protein sequences now have an experimental or a modeled structure. It has therefore become essential to develop fast algorithms capable of detecting non-covalent interactions not only within proteins but also in protein-protein, protein-DNA, protein-RNA, and protein-ligand complexes. Interactions involving aromatic compounds, particularly their $\pi$ molecular orbitals, hold unique significance among molecular interactions due to the electron delocalization, which is known to play a key role in processes such as protein aggregation. In this paper, we present PInteract, an algorithm that detects $\pi$-involving interactions in input structures based on geometric criteria, including $\pi$-$\pi$, cation-$\pi$, amino-$\pi$, His-$\pi$, and sulfur-$\pi$ interactions. In addition, it is capable of detecting chains and clusters of $\pi$ interactions as well as particular recurrent motifs at protein-DNA and protein-RNA interfaces, called stair motifs, consisting of a particular combination of $\pi$-$\pi$ stacking, cation/amino/His-$\pi$ and H-bond interactions. Full article

A theoretical study was performed using Density Functional Theory (DFT) to investigate the impact of π-conjugated aliphatic chain growth on the chemical and electronic properties of hybrid antimony pentachloride salts with pyridine- and imidazolium-based cations. Ten molecular systems were optimized to determine their ground-state geometry. Using conceptual DFT, parameters such as chemical hardness, electrophilicity index, electroaccepting power, and electrodonating power were studied. The energy gap was obtained for all ten molecular systems, ranging from −4.038 to −3.706 eV as the chain length increased, favoring intramolecular charge transfer in long-chain systems. Natural bond orbital (NBO) analysis showed charge redistribution between anion and cation as the π-conjugated aliphatic chain grows. At the same time, non-covalent interaction (NCI) studies revealed key attractions and repulsive interactions, such as H···Cl and Cl···π, which are modulated by chain length. These results demonstrate that the structural modification of the cation allows for the fine-tuning of the electronic properties of ionic liquids (ILs). Increasing the conjugated aliphatic chain length was observed to reduce the chemical hardness and electrophilicity index, as well as affecting the Egap of the molecular systems. This work demonstrates that there is an optimal size for the inorganic ion, allowing it to form an optimal IL compound. Full article

Klebsiella oxytoca originating from shellfish Scapharca subcrenata contains a number of virulence-related genes. In this study, we investigated its pathogenicity using a murine intestinal infection model and predicted its antibacterial compounds and targets via molecular docking analysis. The results revealed that the intake of K. oxytoca 8-2-11 strain (10⁹ CFU/day) via oral gavage for 7 days reduced the average body weight of the mice. The bacterium was present in fecal samples but absent from blood, lung, and liver samples from the mice. The intake of K. oxytoca 8-2-11 significantly altered colon bacteriota, with reduced abundance of Firmicutes, Lachnospiraceae, Lactobacillaceae, Lactobacillus, and Lactobacillus murinus, and increased in Bacteroidota, Muribaculaceae, and Alistipes (p < 0.05). Forty-four bioactive compounds in Scutellaria baicalensis and Forsythia suspensa were screened for docking with 117 potential virulence factors (VFs) in K. oxytoca 8-2-11. The compound baicalin displayed higher binding affinity toward these VFs, with the lowest mean binding energy (−8.4 kcal/mol). Baicalin was able to bind to key VFs in biofilm formation and adherence/motility (e.g., Mrks and EcpA) via forming stable hydrogen bonds, π-stacking, and π-cation interaction. In vitro, baicalin inhibited the bacterial growth and biofilm formation. This study establishes the first murine infection model using aquatic animal-derived K. oxytoca, and it provides candidate antibacterial compounds and targets for control of K. oxytoca infections. Full article

In this study, the design and synthesis of a novel series of cinnamic acid and 1,2,4-triazole hybrids were reported, aiming to enhance antioxidant and lipoxygenase inhibitory activities through pharmacophore combination. Cinnamic acid derivatives and 1,2,4-triazoles exhibit a broad spectrum of biological activities; therefore, by synthesizing hybrid molecules, we would like to exploit the beneficial characteristics of each scaffold. The general synthetic procedure comprises three synthetic steps, starting from the reaction of appropriate substituted cinnamic acid with hydrazine monohydrate in acetonitrile with cyclohexane and resulting in the formation of hydrazides. Consequently, the hydrazides reacted with phenylisothiocyanate under microwave irradiation conditions. Then, cyclization proceeded to the 1,2,4-triazole after the addition of NaOH solution and microwave irradiation. All the synthesized derivatives have been studied for their ability (a) to interact with the free radical DPPH, (b) inhibit lipid peroxidation induced by AAPH, and (c) inhibit soybean lipoxygenase. The synthesized derivatives have shown significant antioxidant activity and have been proved to be very good lipoxygenase inhibitors. Compounds 4b and 4g (IC₅₀ = 4.5 μM) are the most potent within the series followed by compound 6a (IC₅₀ = 5.0 μM). All the synthesized derivatives have been subjected to docking studies related to soybean lipoxygenase. Compound 4g exhibited a docking score of −9.2 kcal/mol and formed hydrophobic interactions with Val126, Tyr525, Lys526, Arg533, and Trp772, as well as a π−cation interaction with Lys526. Full article

Four novel crystalline architectures based on benzo[c]cinnolininium trifluoromethanesulonate salts, [C₁₂H₉N₂]⁺[CF₃SO₃]⁻, have been isolated as single-crystals, and their structures have been determined by X-ray diffraction analysis. The formation of the new salts results from reactions involving the dimeric hydroxo di-n-butylstannane trifluoromethanesulfonato complex [n-Bu₂Sn(OH)(H₂O)(CF₃SO₃)]₂ (1) and benzo[c]cinnoline (C₁₂H₈N₂, BCC). Organic salts I, II, III, and IV were crystallized through slow evaporation at room temperature from a mixture of toluene/dichloromethane. The cystallographic structures of I, II, and IV exhibit the presence of monoprotonated benzo[c]cinnolinium cations in interactions with a free benzo[c]cinnoline molecule through N–H···N hydrogen bonding, while for salt III, the monoprotonated cation directly interacts with the CF₃SO₃⁻ anion via an N–H···O interaction. For all four salts, aromatic π-π interactions involving rings of various components (free benzo[c]cinnoline molecule, benzo[c]cinnolinium cation, toluene molecule), combined with weak C–H···O and C–H···F interactions implying the trifluoromethanesulfonate anion, promote the solid-state self-assembly of supramolecular stacks. In parallel to the formation of benzo[c]cinnolinium based-salts, organotin(IV) 1 was converted into a distannoxane compound, ²_∞{[n-Bu₂(μ-OH)SnOSn(μ-η²-O₃SCF₃)n-Bu₂]₂[n-Bu₂(η¹-O₃SCF₃)SnOSn(μ-OH)n-Bu₂]₂} (3), which was also isolated as a single crystal and whose crystallographic structure was previously established by us. Full article

Enhanced oil recovery (EOR) via CO₂ flooding is a promising strategy for improving hydrocarbon recovery and carbon sequestration, yet the influence of pH on solid–liquid interfacial interactions in quartz-dominated reservoirs remains poorly understood. This study employs molecular dynamics (MD) simulations to investigate the pH-dependent adsorption behavior of crude oil components on quartz surfaces and its impact on CO₂ displacement mechanisms. Three quartz surface models with varying ionization degrees (0%, 9%, 18%, corresponding to pH 2–4, 5–7, and 7–9) were constructed to simulate different pH environments. The MD results reveal that aromatic hydrocarbons exhibit significantly stronger adsorption on quartz surfaces at high pH, with their maximum adsorption peak increasing from 398 kg/m³ (pH 2–4) to 778 kg/m³ (pH 7–9), while their alkane adsorption peaks decrease from 764 kg/m³ to 460 kg/m³. This pH-dependent behavior is attributed to enhanced cation–π interactions that are facilitated by Na⁺ ion aggregation on negatively charged quartz surfaces at high pH, which form stable tetrahedral configurations with aromatic molecules and surface oxygen ions. During CO₂ displacement, an adsorption–stripping–displacement mechanism was observed: CO₂ first forms an adsorption layer on the quartz surface, then penetrates the oil phase to induce the detachment of crude oil components, which are subsequently displaced by pressure. Although high pH enhances the Na⁺-mediated weakening of oil-surface interactions, which leads to a 37% higher diffusion coefficient (8.5 × 10⁻⁵ cm²/s vs. 6.2 × 10⁻⁵ cm²/s at low pH), the tighter packing of aromatic molecules at high pH slows down the displacement rate. This study provides molecular-level insights into pH-regulated adsorption and CO₂ displacement processes, highlighting the critical role of the surface charge and cation–π interactions in optimizing CO₂-EOR strategies for quartz-rich reservoirs. Full article

This study focuses on the search for new effective synthetic antimicrobial compounds as a tool against the widespread presence of microorganisms resistant to existing drugs. Five derivatives of [1,3]thiazolo[3,2-b][1,2,4]triazoles were synthesized using an accessible protocol based on electrophilic heterocyclization and were characterized using infrared (FTIR) and nuclear magnetic resonance (NMR) spectroscopies, and their in vitro antimicrobial and antifungal activities were evaluated using the agar plate diffusion method and the microdilution plate procedure. Both antibacterial (Gram-positive and Gram-negative) and antifungal activities were found for the examined samples. The minimum inhibitory concentration (MIC) varied from 0.97 to 250 µg/mL, and the minimum bactericidal concentration (MBC) from 1.95 to 500 µg/mL. Compound 2a showed good antifungal action against Candida albicans and Saccharomyces cerevisiae with minimum fungicidal concentration (MFC) 125 and MIC 31.25 µg/mL. The molecular docking revealed that the 2-heptyl-3-phenyl-6,6-trimethyl-5,6-dihydro-3H-[1,3]thiazolo[3,2-b][1,2,4]triazol-7-ium cation stands out as a highly promising candidate for further investigation due to a wide range of interactions, including conventional hydrogen bonds, π–σ, π–π T-shaped, and hydrophobic alkyl interactions. The synthesis and preliminary evaluation of [1,3]thiazolo[3,2-b][1,2,4]triazoles yielded promising antimicrobial and antifungal candidates. The diverse interaction profile of the 2-heptyl derivative salt allows this compound’s selection for further biological studies. Full article

Two-dimensional (2D) crystals which present unconventional stoichiometries on graphene surfaces in ambient conditions, such as Na₂Cl, Na₃Cl, and CaCl, have attracted significant attention in recent years due to their electronic structures and abnormal cation–anion ratios, which differ from those of conventional three-dimensional crystals. This unconventional crystallization is attributed to the cation–π interaction between ions and the π-conjugated system of the graphene surface. Consequently, their physical and chemical properties—including their electrical, optical, magnetic, and mechanical characteristics—often differ markedly from those of conventional crystals. This review summarizes the recent progress made in the fabrication and analysis of the structures, distinctive features, and applications of these 2D unconventional stoichiometry crystals on graphene surfaces in ambient conditions. Their special properties, including their piezoelectricity, metallicity, heterojunction, and room-temperature ferromagnetism, are given particularly close attention. Finally, some significant prospects and further developments in this exciting interdisciplinary field are proposed. Full article