Search Results (78)

Relaxation behavior of water confined in reverse micelles under temperature-induced micelle clustering is undertaken using broadband dielectric spectroscopy in frequency range 1 Hz–20 GHz. All microemulsion systems with sufficiently noticeable micelle water pool (water/surfactant molar ratio W > 10) depict three relaxation processes, in low, high and microwave frequencies, anchoring with relaxation of shell (bound) water, orientation of surfactant anions at water-surfactant interface and relaxation of bulk water confined in reverse micelles. The analysis of dielectric relaxation processes in AOT-based w/o microemulsions under temperature induced clustering of reverse micelles were made according to structural information obtained in NMR and conductometry experiments. The “wait and switch” relaxation mechanism was applied for the explanation of results for water in the bound and bulk states under spatial limitation in reverse micelles. It was shown that surfactant layer predominantly influences the bound water. The properties of water close to AOT interface are determined by strong interactions between water and ionic AOT molecules, which perturb water H-bonding network. The decrease in micelle size causes a weakening of hydrogen bonds, deformation of its steric network and reduction in co-operative relaxation effects. Full article

Water within coal reservoirs exerts dual effects on methane adsorption–desorption by competing for adsorption sites and reducing permeability. The bound water effect, caused by coal wettability, significantly constrains coalbed methane (CBM) production, rendering investigations into coal wettability crucial for efficient CBM development. Compared with other geological formations, coals are characterized by a highly developed microporous structure, making the CO₂ sequestration mechanism in coal seams closely linked to the microscale interactions among gas, water, and coal matrixes. However, the intrinsic mechanisms remain poorly understood. In this study, molecular dynamics simulations are employed to investigate the wettability behaviors of CO₂, CH₄, and water on different coal matrix surfaces under varying temperature and pressure conditions, for coal macromolecules representative of four coal ranks. The study reveals the evolution of water wettability in response to CO₂ and CH₄ injection, identifies wettability differences among coal ranks, and analyzes the microscopic mechanisms governing wettability. The results show the following: (1) The contact angle increases with gas pressure, and the variation in wettability is more pronounced in CO₂ environments than in CH₄. As pressure increases, the number of hydrogen bonds decreases, while the peak gas density of CH₄ and CO₂ increases, leading to larger contact angles. (2) Simulations under different temperatures for the four coal ranks indicate that temperature has minimal influence on low-rank Hegu coal, whereas for higher-rank coals, gas adsorption on the coal surface increases, resulting in reduced wettability. Interfacial tension analysis further suggests that higher temperatures reduce water surface tension, cause dispersion of water molecules, and consequently improve wettability. Understanding the wettability variations among different coal ranks under variable pressure–temperature conditions provides a fundamental model and theoretical basis for investigating deep coal seam gas–water interactions and CO₂ geological sequestration mechanisms. These findings have significant implications for the advancement of CO₂-ECBM technology. Full article

Prion diseases such as chronic wasting disease involve the conformational conversion of the cellular prion protein (PrP^C) into its misfolded, β-rich isoform (PrP^Sc). While chemical denaturants such as guanidine hydrochloride (GdnHCl) and urea are commonly used to study this process in vitro, their distinct molecular effects on native and misfolded PrP conformers remain incompletely understood. In this study, we employed 500 ns all-atom molecular dynamics simulations and essential collective dynamics analysis to investigate the differential effects of GdnHCl and urea on a composite PrP^C/PrP^Sc system, where white-tailed deer PrP^C interfaces with a corresponding PrP^Sc conformer. GdnHCl was found to preserve interfacial alignment and enhance β-sheet retention in PrP^Sc, while urea promoted partial β-strand dissolution and interfacial destabilization. Both denaturants formed transient contacts with PrP, but urea displaced water hydrogen bonds more extensively. Remarkably, we also observed long-range dynamical coupling across the PrP^C/PrP^Sc interface and between transiently bound solutes and distal protein regions. These findings highlight distinct, denaturant-specific mechanisms of protein destabilization and suggest that localized interactions may propagate non-locally via mechanical or steric pathways. Our results provide molecular-scale insights relevant to prion conversion mechanisms and inform experimental strategies using GdnHCl and urea to modulate misfolding processes in vitro. Full article

Microbial transglutaminase (mTG) is most frequently utilized in order to increase the gelling properties of soybean protein isolate (SPI), but there are still some limitations of mTG-based hydrogel fabrication technology. Therefore, we aimed to develop a dual modification technique based on enzyme plus organic acid treatment to fabricate SPI hydrogels with high gel strength and stability. Our results showed that mTG plus glucose-δ-lactone (GDL), lactobionic acid (LBA) or maltobionic acid (MBA) treatment could significantly improve the gel strength, textural properties, and water-holding capacity of SPI hydrogels. Also, the addition of these organic acids remarkably reduced the surface hydrophobicity (H₀) and intrinsic fluorescence as well as increased the storage modulus (G′), loss modulus (G″) values, average particle size, and the absolute value of zeta potential of samples. GDL, LBA, or MBA greatly increased the β-sheet level and decreased the α-helix level in hydrogels, as well as dissociated 11S subunits of SPI into 7S subunits. Notably, covalent interactions, hydrogen bonding, and hydrophobic interactions of three organic acids with SPI, as well as the effects of organic acids on the interactions among the intramolecular and intermolecular forces of SPI molecules, contributed to their promoting effects on the formation of hydrogels. The LF-NMR and SEM analyses confirmed the effects of GDL, LBA, and MBA on converting the free water into immobilized and bound water as well as forming a dense stacked aggregate structure. Therefore, GDL, LBA, and MBA are promising agents to be combined with mTG in the fabrication of SPI hydrogels with high gel strength and stability. Full article

Formononetin is widely used in anti-tumor research, but its poor water solubility leads to low absorption and poor utilization efficiency in vivo, limiting further development. The triphenylphosphine cation was partially attached to the 7-position hydroxyl group of formononetin to specifically target it into the mitochondria of tumor cells to enhance the anti-tumor effect. Detailed structural characterization via ¹H-NMR and ¹³C-NMR analysis confirmed the physical properties and chemical structures of 21 newly synthesized derivatives. The effects of these derivatives on tumor cells were assessed by in vitro and computational methods. MTT results from four tumor cell lines showed that formononetin derivatives containing triphenylphosphine had stronger anti-tumor activity than formononetin and exhibited more cytotoxic effects in cancer cells than in normal cells. In particular, the final product 2c (IC₅₀ = 12.19 ± 1.52 μM) showed more potent anti-tumor activity against A549 cells. It was also superior to formononetin and 5-FU. To identify the potential biological targets, the core-expressed gene SHMT2 in lung cancer mitochondria was screened using network pharmacology technology, and molecular docking analysis confirmed the stable binding of the end products to the amino acid residues of the core genes through the formation of hydrogen bonds and via other interactions. In addition, molecular docking simulations further confirmed that the end product exhibited excellent stability when bound to SHMT2. These results suggest that triphenylphosphine-containing formononetin derivatives are worthy of further exploration in the search for novel drug candidates for the treatment of cancer. Full article

An outstanding adsorbent, such as the metal–organic framework (MOF) MIL-101 (Cr), was employed to study the adsorption of two dyes, namely reactive red 2 (RR2) and reactive blue 19 (RB19). Experimental adsorption data were retrieved at T = 25, 35 and 45 °C and analyzed to define the adsorption mechanism of these dyes. A modeling approach based on a double-layer model derived from statistical physics was used. The maximum adsorption capacity (MAC) was found to be 875, 954 and 1002 mg/g for RR2 and 971, 1093 and 1148 mg/g for RB19, at T = 25, 35 and 45 °C, respectively. These values indicate that MIL-101 (Cr) exhibits outstanding performance in removing potential water pollutants such as the RR2 and RB19 dyes. The possible orientations of the RR2 and RB19 dyes upon adsorption were determined by analyzing the number of dye molecules bound per MIL-101 (Cr) active sites during the adsorption process. It was found that the RR2 dye was removed via a mixed parallel and non-parallel orientation on MIL-101 (Cr), while RB19 was removed via an inclined orientation at higher temperatures. The adsorption mechanism suggested that MIL-101 (Cr) site density was reduced due to an exothermic effect, which decreases the number of active sites participating in dye adsorption, even though the reduction in water adsorption may be attributed to the overall endothermic behavior. From the adsorption energy (AE) and the chemical structure of MIL-101 (Cr) and both dyes, it was concluded that hydrogen bonds, Van der Waals forces and π-π stacking are involved in the dye removal process. This research provides new physical insights into the adsorption mechanism of two relevant dyes on an outstanding adsorbent such as the MIL-101 (Cr) MOF. Full article

Background: Alzheimer’s disease (AD) is a multifactorial neurodegenerative disorder characterised by the accumulation of neurotoxic substances in the brain, ultimately leading to progressive cognitive decline. The complex aetiology and involvement of multiple molecular targets in AD pathogenesis have made discovering effective therapeutic agents particularly challenging. Targeting multiple proteins simultaneously with a single therapeutic agent may offer a promising strategy to address the disease’s multifaceted nature. Methods: This study employed advanced computational methodologies to perform multitargeted molecular docking of FDA-approved drugs against four key AD-associated proteins implicated in disease progression. Among the screened compounds, Rebamipide—a drug conventionally used for treating gastrointestinal disorders—demonstrated notable binding affinities across all targets. Pharmacokinetic predictions, interaction fingerprinting, WaterMap analysis, density functional theory (DFT) calculations, and 100 ns MD simulations were performed for each protein–ligand complex to evaluate its multitarget potential. Results: Rebamipide bound effectively to the NR1 ligand-binding core, suggesting modulation of glutamatergic signalling while reducing β-secretase production and regulating neurotransmitter homeostasis through inhibiting monoamine oxidase-A. Furthermore, Rebamipide enhanced cholinergic neurotransmission by inhibiting human acetylcholinesterase, potentially improving cognitive function. Pharmacokinetic analyses confirmed favourable drug-like properties. Molecular interaction fingerprints revealed consistent hydrogen bonding, hydrophobic contacts, and π-π stacking interactions. WaterMap analysis indicated thermodynamically favourable water displacement upon binding, enhancing ligand affinity. DFT analysis of Rebamipide showed a 4.24 eV HOMO-LUMO gap, with ESP values ranging from −6.63 × 10⁻² to +6.63 × 10⁻² A.U., indicating reactive sites. TDDFT predicted strong UV absorption at 314 nm with a peak intensity of ~6500 L mol⁻¹ cm⁻¹. MD simulations over 100 ns demonstrated minimal structural deviations and stable ligand–protein complexes, reinforcing its multitarget efficacy. Conclusions: The comprehensive in silico investigation highlights Rebamipide as a promising multitargeted therapeutic candidate for Alzheimer’s disease. Its ability to modulate multiple pathogenic pathways simultaneously underscores its potential utility; however, these computational findings warrant further experimental validation to confirm its efficacy and therapeutic relevance in AD. Full article

In this study, complexes of pregelatinized Chinese yam starch with ferulic acid (PCYS+FA) were prepared using a boiling water bath, with varying levels of Chinese yam starch (CYS) and ferulic acid (FA). The investigation focused on the effects of FA addition (3%, 9%, and 15%) on the physicochemical properties and structure of PCYS+FA complexes. The solubility, swelling, and water-holding capacity of PCYS+FA were compared with those of CYS, with the solubility and swelling showing a gradual enhancement with increasing FA content. The incorporation of FA reduced the thermal stability of CYS, decreasing the initial degradation temperature from 245.94 °C (CYS) to 228.17 °C (PCYS+15%FA). Infrared spectroscopy revealed that CYS and FA were bound through non-covalent intramolecular hydrogen bonding. Furthermore, X-ray diffractograms showed that FA and CYS formed a V-type complex, in which the crystallinity of PCYS reached a minimum of 3.72%, and the degree of molecular ordering was reduced. Scanning electron microscopy analysis demonstrated that FA adhered to the surface of starch granules, resulting in the formation of pores that facilitated the entry of FA molecules into the internal crystal region of starch, allowing them to interact with starch molecules. Full article

Mismatched T:G base pairs can arise during de novo replication as well as base excision repair (BER). In particular, the action of the gap-filling polymerase β (Polβ) can generate a T:G pair as well as a nick in the DNA backbone. The processing of a nicked T:G mispair is poorly understood. We are interested in understanding whether the T:G-specific DNA glycosylase MBD4 can recognize and process nicked T:G mismatches. We have discovered that MBD4 binds a nicked T:G-containing DNA, but does not cleave thymine opposite guanine. To gain insight into this, we have determined a crystal structure of human MBD4 bound to a nicked T:G-containing DNA. This structure displayed the full insertion of thymine into the catalytic site and the recognition of thymine based on the catalytic site’s amino acid residues. However, thymine excision did not occur, presumably due to the inactivation of the catalytic D560 carboxylate nucleophile via a polar interaction with the 5′-hydrogen phosphate of the nicked DNA. The nicked complex was greatly stabilized by an ordered water molecule that formed four hydrogen bonds with the nicked DNA and MBD4. Interestingly, the arginine finger R468 did not engage in the phosphate pinching that is commonly observed in T:G mismatch recognition complex structures. Instead, the guanidinium moiety of R468 made bifurcated hydrogen bonding interactions with O6 of guanine, thereby stabilizing the estranged guanine. These observations suggest that R468 may sense and disrupt T:G pairs within the DNA duplex and stabilize the flipped-out thymine. The structure described here would be a close mimic of an intermediate in the base extrusion pathway induced by DNA glycosylase. Full article

Phenolic acids have a positive effect on the processing quality of myofibrillar protein (MP) gels. However, in this study, the addition of ferulic acid (FA) did not have a positive effect on MP gels. To address this issue, we performed the addition and observed the effects on the structure of MP gels by both surface coating and internal cross-linking: addition of FA alone, addition of α-cyclodextrin (CD) to encapsulate FA (MP-FA/CD), and addition of Fe(III) to form a metal–phenolic network structure (Fe @MP-FA) and a metal–cyclodextrin–phenolic acid structure (Fe@MP-FA /CD). It was found that both Fe @MP-FA formed by surface coating and internal cross-linking were able to improve the textural properties of MP gels, including hardness, elasticity, chewability, adhesion, etc. FA effectively promoted the conversion of some of the non-fluidizable water to the bound water morphology, and the addition of Fe(III) effectively enhanced this trend. In particular, the composite network structure formed by Fe@MP-FA/CD more significantly promoted the conversion to bound water and improved the water retention of the gel. Hydrophobic interactions and hydrogen bonding in non-covalent bonding as well as disulfide bonding in covalent bonding were always the main factors promoting the formation of gels from MP after different additions. Meanwhile, different gel treatments lead to changes in the structure of different proteins. Internal cross-linking with the addition of FA promotes protein oxidation, whereas CD reduces the occurrence of oxidation and promotes a homogeneous gel structure. Surface coating with the addition of FA/CD resulted in a reduction in pores in the MP gels and a denser gel structure. However, the addition of internal cross-linking resulted in a gel with a loose and rough network structure. In this study, we compared the common methods of gel enhancement, with the objective of providing a reference for the improvement in the gel texture of meat products. Full article

The interaction of sodium phytate hydrate C₆H₁₈O₂₄P₆·xNa·yH₂O (phytNa) with Cu(OAc)₂·H₂O and 1,10-phenanthroline (phen) led to the anionic tetranuclear complex [Cu₄(H₂O)₄(phen)₄(phyt)]·2Na⁺·2NH₄⁺·32H₂O (1), the structure of the latter was determined by X-ray diffraction analysis. The phytate 1 is completely deprotonated; six phosphate⁻ fragments (with atoms P1–P6) are characterized by different spatial arrangements relative to the cyclohexane ring (1a5e conformation), which determines two different types of coordination to the complexing agents—P1 and P3, P4, and P6 have monodentate, while P2 and P5 are bidentately bound to Cu²⁺ cations. The molecular structure of the anion complex is stabilized by a set of strong intramolecular hydrogen bonds involving coordinated water molecules. Aromatic systems of phen ligands chelating copper ions participate in strong intramolecular and intermolecular π-π interactions, further contributing to their association. At the supramolecular level, endless stacks are formed, in the voids of which sodium and ammonium cations and water molecules are present. The stability of 1 in the presence of human serum albumin (HSA) was investigated using Electron Paramagnetic Resonance (EPR) spectroscopy. Continuous wave (CW) EPR spectra in water/glycerol frozen solution clearly indicate a presence of an exchange-coupled Cu(II)-Cu(II) dimeric unit, as well as a Cu(II) monomer-like signal arising from spins sufficiently distant from each other, with comparable contributions of two types of signals. In the presence of albumin at a 1:1 ratio (1 to albumin), the EPR spectrum changes significantly, primarily due to the reduced contribution of the S = 1 fraction showing dipole–dipole splitting. The biological activity of 1 in vitro against the non-pathogenic (model for Mycobacterium tuberculosis) strain of Mycolicibacterium smegmatis is comparable to the first-line drug for tuberculosis treatment, rifampicin. Full article

Succinimide residues formed spontaneously from aspartic acid (Asp) and asparagine (Asn) residues in proteins and peptides are stereochemically unstable, undergoing partial l-to-d stereoinversion, and this is responsible for the d-Asp and d-β-Asp residues found in long-lived proteins. These stereoinverted abnormal amino acid residues are believed to be related to aging and some age-related diseases such as cataracts. Although the succinimide stereoinversion is nonenzymatic, a catalyst is required for it to occur at physiological temperature. In this study, it was found by density functional theory (DFT) calculations that a hydrogen phosphate ion (HPO₄²⁻) can effectively catalyze the stereoinversion of the succinimide intermediate. The HPO₄²⁻ ion abstracts a proton from the asymmetric carbon atom of the succinimide residue to form an enolate intermediate. Then, while the resultant dihydrogen phosphate ion (H₂PO₄⁻) remains bound to the enolate ion, a water molecule donates a proton to the enolate intermediate on the opposite side from the phosphate (which is the rate-determining step) to produce the inverted carbon atom. The calculated activation barrier (ca. 90 kJ mol⁻¹) is consistent with a slow in vivo reaction. The present found mechanism can be termed the “unsymmetrical S_E1” or “pseudo-S_E2” mechanism. Full article

Fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), and Scanning electron microscopy (SEM) were used to study the effects of heat treatments and water removal by freeze-drying after different time intervals (6, 12, 24, 48, and 72 h) on the molecular structure of potato tubers. SEM images show structural differences between raw (RP), microwaved (MP), and boiled potato (BP). MP showed a cracked structure. BP was able to re-associate into a granule-like structure after 6 h of freeze-dying, whereas RP had dried granules within a porous matrix after 24 h of freeze-drying. These results are consistent with the moisture content and FTIR results for MP and BP, which demonstrated dried spectra after 6 h of freeze-drying and relatively coincided with RP results after 24 h of freeze-drying. Additionally, three types of hydrogen bonds have been characterized between water and starch, and the prevalence of water very weakly bound to starch has also been detected. The relative crystallinity (RC) was increased by thermal treatment, whereby microwaving recorded the highest value. A comparison of the FTIR and XRD results indicated that freeze-drying treatment overcomes heat effects to generate an integral starch molecule. Full article

The impact of hot air drying temperature on instant dough sheets’ qualities was investigated based on water migration and gluten network structure changes. The results revealed that the drying process redistributed the hydrogen proton, with deeply bound water accounting for more than 90%. The T₂ value decreased as the drying temperature increased, effectively restricting moisture mobility. Meanwhile, microstructural analysis indicated that instant dough sheets presented porous structures, which significantly reduced the rehydration time of instant dough sheets (p < 0.05). In addition, elevated drying temperatures contributed to the cross-linking of proteins, as evidenced by increased GMP and disulfide bond content (reaching a maximum at 80 °C), which improved the texture and cooking properties. Hence, the water mobility was effectively reduced by controlling the drying temperature. The temperature had a facilitating impact on promoting the aggregation of the gluten network structure, which improved the quality of the instant dough sheets. Full article

Polyvinyl alcohol (PVA) hydrogels find applications in various fields, including machinery and tissue engineering, owing to their exceptional mechanical properties. However, the mechanical properties of PVA hydrogels are subject to alteration due to environmental factors such as temperature, affecting their prolonged utilization. To enhance their lifespan, it is crucial to investigate their aging mechanisms. Using physically cross-linked PVA hydrogels, this study involved high-temperature accelerated aging tests at 60 °C for 80 d and their performance was analyzed through macroscopic mechanics, microscopic morphology, and microanalysis tests. The findings revealed three aging stages, namely, a reduction in free water, a reduction in bound water, and the depletion of bound water, corresponding to volume shrinkage, decreased elongation, and a “tough-brittle” transition. The microscopic aging mechanism was influenced by intermolecular chain spacing, intermolecular hydrogen bonds, and the plasticizing effect of water. In particular, the loss of bound water predominantly affected the lifespan of PVA hydrogel structural components. These findings provide a reference for assessing and improving the lifespan of PVA hydrogels. Full article