Search Results (157)

In this paper we validate Group Contribution (GC) parameters for substituted phenols and dihydroxybenzenes including catechol, resorcinol and hydroquinone with respect to a recently developed Group Contribution method for estimating the heat of formation of organic compounds with chemical accuracy (1 kcal/mol). For the compounds studied, we found differences greater than this threshold between experimental data from different publications. Using quantum mechanical methods in conjunction with common knowledge from physical organic chemistry, we were able to validate the GC model values and thereby extend the applicability range of the previously developed model. It could be concluded that most GC-predicted values can be considered trustworthy, assuming the B3LYP correction for steric interaction between ortho t-butyl and hydroxyl groups is included. As with earlier studies, we found that G4 quantum-calculated values can serve as a reliable source of gas-phase heats of formation of organic compounds. Full article

To address the common drawbacks of polyamine-based CO₂ absorbents, such as high viscosity and precipitation at high CO₂ loading, a novel liquid–liquid biphasic absorbent composed of triethylenetetramine (TETA), 1-(2-aminoethyl)piperazine (AEP), N,N-dimethylacetamide (DMAC), and H₂O was developed in this study. By comprehensively evaluating CO₂ saturation loading, phase separation behavior, rheological properties of the CO₂-rich phase, precipitation suppression, and desorption–regeneration performance, the optimal absorbent formulation was identified as 20 wt% TETA + 10 wt% AEP + 40 wt% DMAC + 30 wt% H₂O. The optimized system enabled more than 98% of the CO₂ absorption products to be concentrated in the lower phase, which accounted for only 56% of the total liquid volume. Compared with the AEP-free TETA/DMAC/H₂O system, the optimized AEP-modified absorbent effectively eliminated precipitation and reduced the viscosity of the CO₂-rich phase to 62.3 mPa·s, while also improving the desorption behavior and cyclic stability of the system. In addition, ¹³C NMR analysis suggested that the salting-out effect is the main driving force for phase separation, with ionic products preferentially enriched in the aqueous phase to form the CO₂-rich lower phase. AEP contributes to viscosity reduction, precipitation suppression, and enhanced regeneration by weakening carbamate aggregation through steric hindrance and promoting bicarbonate formation. Full article

Hydrolyzed polyacrylamide stabilized oil-in-water emulsions are highly persistent because the polymer strengthens both continuous-phase rheology and the oil–water interfacial film, making demulsification difficult in polymer-flooding produced liquids. Here, an hydrolyzed polyacrylamide degrading bacterium, Delftia lacustris EPDB-8, was isolated, and its ability to destabilize hydrolyzed polyacrylamide-containing emulsions was investigated from molecular, bulk rheological, and interfacial perspectives. EPDB-8 effectively degraded HPAM, causing marked reductions in total organic carbon, total nitrogen, absolute zeta potential, and polymer molecular weight, with an approximately 63-fold decrease after 7 days. SEM, FT-IR, and GPC analyses showed that biodegradation proceeded through deamidation and random chain scission, collapsing the polymer network and generating low-molecular-weight fragments. Driven by bacterial hydrolyzed polyacrylamide degradation, these structural alterations disrupted the viscoelastic composite interfacial film formed by hydrolyzed polyacrylamide and indigenous surface-active species, directly causing emulsion stabilization to shift from polymer-assisted viscous and steric protection to a less effective asphaltene-dominated interfacial structure and thereby accelerating droplet aggregation, coalescence, and phase separation. Although bacterial cells exerted a transient particle-assisted interfacial effect, long-term emulsion stability remained governed by polymer integrity. This study establishes a mechanistic link between hydrolyzed polyacrylamide biodegradation and the rheological and interfacial evolution governing emulsion breakdown, providing a cost-effective and environmentally benign biological strategy for demulsification and treatment of polymer-flooding produced water. These findings offer practical guidance for the design of microbial-based produced-water treatment systems and contribute to the sustainable management of oilfield wastewater generated during enhanced oil recovery operations. Full article

Intermolecular interactions play an important role in the formation and stability of co-crystals. In this study, the interaction behaviour of theophylline in co-crystal structures was systematically analysed using data from the Cambridge Structural Database. A total of fifty-three theophylline co-crystal structures were investigated and classified according to their intermolecular interaction motifs. A structured interaction scheme was developed to describe the accessible interaction sites of theophylline, including classical and non-classical hydrogen bonds, as well as halogen bonds and π∙∙∙π interactions. The study revealed theophylline’s high versatility in forming intermolecular interactions, resulting in twenty interaction patterns. Three dominant motifs were identified as occurring most frequently. The results indicate that steric effects influence the accessibility of specific interaction sites, particularly limiting interactions at the carbonyl group located between the two methyl groups. Hirshfeld surface analysis revealed that O∙∙∙H and H∙∙∙H interactions contribute most significantly to the intermolecular interactions in the analysed structures. Full article

To overcome graphene aggregation in aqueous nanofluids, polycarboxylate-modified structural graphene (PSG) was synthesized via surface functionalization. Characterizations indicate that the modification preserves the 3D hierarchical porous framework while ensuring exceptional dispersion stability through steric hindrance and enhanced hydrophilicity. Convective heat transfer evaluations demonstrated remarkable enhancement; notably, the 0.1 wt% PSG nanofluid achieved a 46% increase in the heat transfer coefficient over pure water at Re = 4000. Molecular dynamics simulations further revealed the underlying interfacial mechanisms. The surface-anchored oxygen-containing groups induce a dense, hydrogen-bonded hydration layer that restricts local water diffusion. This highly ordered interfacial structure may facilitate vibrational energy exchange across the solid–liquid boundary. Together with the intrinsic high-conductivity 3D skeleton, these microscopic interactions are likely to contribute to the enhanced macroscopic thermal performance, providing a promising framework for designing advanced graphene-based thermal management fluids. Full article

Synthetic polymers are widely used in stone conservation, yet their long-term biological stability remains insufficiently evaluated. This study investigates the microbial susceptibility of three commonly used acrylic consolidants, Paraloid B-72, B-66, and B-44, applied to deteriorated limestone. Bacteria, fungi, and actinomycetes were isolated from a deteriorated limestone false door and screened for acid production. From each microbial group, only the strong acid-producing isolates were selected for further investigation, including evaluation of their ability to utilize the three Paraloid resins as sole carbon sources and their deterioration potential on limestone cubes before and after consolidation. Deterioration was assessed by weight loss, compressive strength testing, stereomicroscopy, scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR). All selected strong acid-producing isolates demonstrated the ability to grow on the tested polymers, confirming their biodegradation potential. Mixed microbial cultures caused greater weight loss and compressive strength reduction than single isolates, attributed to synergistic metabolic interactions. Among the consolidants, Paraloid B-72 showed the highest susceptibility to microbial attack, while Paraloid B-66 exhibited comparatively greater resistance, attributed to the steric hindrance of its isobutyl side groups and higher surface hydrophobicity. FTIR and XRD analyses confirmed ester bond hydrolysis, progressive gypsum formation, and structural alteration of the limestone substrate. These findings demonstrate that acrylic consolidants commonly used in stone conservation are not biologically inert and may actively contribute to biodeterioration under microbial colonization, highlighting the need for developing bio-resistant conservation materials. Full article

The synergistic gelation between xanthan gum (XG) and locust bean gum (LBG) is a classic phenomenon widely adopted for quality control of XG functionality; yet the regulatory roles of XG’s side chain groups—particularly glucuronic acid, whose function remains unexplored—have not been systematically elucidated. In this study, three complementary modification strategies including enzymatic hydrolysis, oxalic acid treatment, and dilute alkali treatment were for the first time combined to precisely modulate the contents of pyruvate, acetyl, and glucuronic acid in XG side chains, constructing a series of XG samples with well-defined gradient structures. Enzymatic hydrolysis and oxalic acid treatment reduced the pyruvate content from 5.80% to 1.05% and 1.42%, respectively, while dilute alkali treatment selectively decreased the acetyl content from 3.97% to 2.58%. The effects were systematically investigated through multi-scale characterization including rheology, texture analysis, scanning electron microscopy and thermogravimetric analysis, combined with correlation analysis. The results revealed that glucuronic acid, together with pyruvate, synergistically enhanced gel network stability through electrostatic interactions and hydrogen bonding. In contrast, acetyl groups acted as negative regulators via steric hindrance, inhibiting hydrogen-bond crosslinking. This study clarifies the distinct functional roles of key XG side chain groups, with the first systematic demonstration of glucuronic acid’s contribution, and provides a theoretical basis for the structure-oriented precise design of XG-based functional gels. Full article

High-liquid-limit clay exhibits pronounced water sensitivity due to the strong electrostatic repulsion and weak interparticle bonding within its microstructure, which often limits its direct engineering uses and complicates the reuse of excavated clayey soils generated during the construction of transportation infrastructure. In this study, inorganic salts (KCl, CaCl₂ and FeCl₃) and carboxyl-containing polymers (PAAS, HPMA and CMC) were screened to construct organic–inorganic composite stabilization systems. Based on the screening results, an organic–inorganic composite system composed of CaCl₂ and sodium polyacrylate (PAAS) was developed to regulate interfacial interactions and induce microstructural reconstruction in clay. The synergistic mechanisms governing particle aggregation and dispersion were systematically investigated through Atterberg limit tests, zeta potential measurements, DLVO theoretical calculations, particle size analysis, scanning electron microscopy (SEM) and immersion disintegration experiments, combined with multivariate statistical modeling. Among the tested salt–polymer formulations, a composite system with 2% CaCl₂ and 0.1% PAAS showed the most favorable overall performance, achieving an optimal balance between electrostatic compression and steric stabilization, leading to enhanced structural integrity and delayed water-induced disintegration. Ca²⁺ ions compress the diffuse double layer and promote particle flocculation, whereas adsorbed PAAS chains introduce steric hindrance and interfacial modification. Their synergistic interaction reconstructs the pore–aggregate framework and regulates the interparticle potential energy landscape. DLVO analysis indicates that the optimized system attains a moderate critical interaction distance (h_c = 7.31 nm) and primary minimum depth (DPM = −2.72 × 10⁻¹⁶ J), reflecting a balanced interfacial bonding state. Multivariate statistical analyses further reveal a dual control pathway, in which consistency primarily governs disintegration duration, with additional contributions from surface electrochemical properties, while surface properties, soil structure and consistency collectively influence disintegration initiation. These findings elucidate the interfacial regulation and structural evolution mechanisms in organic–inorganic composite systems and provide insights into the design of composite modifiers for water-sensitive particulate materials, particularly for the resource reuse of high-liquid-limit clay excavated during the construction of transportation infrastructure and related geotechnical engineering applications. Full article

The colloidal particles present in natural soil and groundwater systems possess distinctive properties that enable them to migrate across solid surfaces, thereby exerting a significant influence on the distribution of pollutants. While the attachment of colloidal particles to solid surfaces has been extensively investigated, the mechanisms governing their detachment under varying hydrochemical conditions remain largely unexplored. The common interaction between montmorillonite colloids and solid medium (Al₂O₃) in soil affects the fate of pollutants such as heavy metals. In our study, Al₂O₃ was used as solid medium to observe the adsorption and desorption behavior of montmorillonite colloids. It was found that the adsorption capacity of Al₂O₃ to montmorillonite colloids could reach 4.71 mg g⁻¹ (pH 5.0 and 10 mM NaCl concentration). X-ray photoelectron spectroscopy analysis shows that montmorillonite colloids react with the Al₂O₃ surface mainly through chemical groups with –O–Si bonds. Desorption experiments show that SDS drives desorption by neutralizing and reversing the surface charge of Al₂O₃, while CTAB directly modifies montmorillonite colloids and introduces steric hindrance to achieve desorption. These research data contribute to a comprehensive understanding of the migration behavior of montmorillonite colloids on solid phases. Full article

This work reports the isolation and structural characterization of 1-(2-aminophenyl)-3-(4-pyridyl)-3-hydroxy-1-propanone (1), a β-hydroxyketone intermediate that crystallized unexpectedly during the base-catalyzed aldol condensation of 2-aminoacetophenone with pyridine-4-carbaldehyde, a reaction intended to afford the corresponding pyridyl chalcone (2). The formation of (1) highlights the sensitivity of Claisen–Schmidt reactions to the electronic and steric features of the substrates and to the applied reaction conditions. Single-crystal X-ray diffraction unambiguously confirmed the molecular structure of (1), revealing a hydrogen-bonding network involving the amino, carbonyl, and β-hydroxyl functionalities. These interactions contribute to the solid-state stabilization of the β-hydroxyketone and hinder its dehydration to chalcone (2). The present results provide experimental insight into the mechanistic landscape of aldol condensations and emphasize the relevance of isolable intermediates as structurally defined precursors for further synthetic transformations. Full article

In situ cancer vaccines activate antitumor immune responses by locally capturing and presenting tumor-derived antigens, in which polymers play a key role as antigen-capturing materials. However, the influence of polymer composition and degree of polymerization (DP) on antigen capture efficiency and protection mechanisms remains insufficiently understood. In this study, the tumor-specific antigen MAGE-A3, highly expressed in esophageal squamous cell carcinoma (ESCC), was employed to investigate antigen capture and stabilization by five representative polymers—chitosan, polyethyleneimine (PEI), alginate, polycaprolactone (PCL), and poly (lactic-co-glycolic acid) (PLGA)—with different DPs, using molecular dynamics simulations and in vitro experiments. All-atom simulations revealed that hydrophobic interactions dominate polymer–antigen binding, while electrostatic interactions from cationic polymers synergistically enhance binding affinity and capture efficiency. Binding free energy analysis showed that van der Waals and electrostatic contributions stabilize the complexes, whereas polar solvation partially counteracts these effects. Experimentally, low-DP chitosan exhibited the highest antigen-capture efficiency (38.9%), attributed to its small molecular size, enabling multipoint binding across the antigen surface. In contrast, high-DP polymers generated pronounced steric hindrance that suppressed antigen–enzyme interactions and inhibited hydrolysis. These findings clarify how polymer composition and chain length jointly regulate antigen capture and protection, providing mechanistic guidance for the rational design of polymer-based in situ cancer vaccines. Full article

Background: Point mutations to the androgen receptor (AR) ligand-binding domain (LBD) are becoming increasingly recognized as a mechanism of therapeutic resistance in castration resistant prostate cancer (CRPC). The present review explores how point mutations induce molecular changes that contribute to the eventual treatment failure of androgen receptor pathway inhibitors (ARPIs) in CRPC. Methods: The PubMed database was searched for structural studies on the AR LBD. Eligible articles included molecular docking analysis and emphasized changes in ligand–receptor interactions after point mutation. Structural data were obtained from the Protein Data Bank (PDB) using the search parameters “Androgen receptor ligand binding domain”, “Homo sapiens”, and “X-ray diffraction”. PDB files of wild-type and point mutant AR LBDs were accumulated for analysis. Results: A functional shift from inhibiting to activating AR has been documented for multiple ARPIs. Crystallography data and in silico evaluation have deciphered how changes in steric hindrance of the AF-2 domain contribute to ARPI loss of function. To combat therapeutic resistance, discovery efforts have begun to consider combination approaches of orthosteric and allosteric inhibitors, as well as compounds that target other AR domains. Although lead compounds have been identified, none have progressed into the clinic. Conclusions: Questions remain regarding the best approach for rationally designing new AR targeting therapeutics. Understanding how structural changes to the AR LBD lead to the failure of clinical therapeutics is a necessary step that should precede drug discovery campaigns. Moreover, computational modeling is a powerful tool that should be leveraged to streamline therapeutic development. Full article

Chronic, dysregulated inflammation contributes to colitis-associated colorectal cancer (CRC), and the cGAS–STING pathway represents a central but therapeutically challenging node because both insufficient and excessive STING activity can be pathogenic. Here, we integrate AlphaFold3 (AF3) receptor modeling, diffusion-based docking, and explicit-solvent molecular dynamics (MD) simulations to characterize how the marine briarane diterpenoid excavatolide B (ExcB) engages the human STING (hSTING) cyclic dinucleotide (CDN)-binding cleft. The structural integrity of the AF3 hSTING model was validated through both intrinsic confidence scores (pLDDT, PAE) and comparative benchmarking against experimental CTD structures (PDB: 4EF5, 6A05). Notably, the local geometries of key pocket-defining residues—including His157, Tyr167, and Thr263—remained consistent with established crystallographic data. Across three independent 100 ns MD replicas, ExcB exhibits a consistent spatial progression from an entrance-proximal pose at the solvent-accessible rim of the cleft (Site-2) to a more embedded, non-canonical corridor on the Cys148-adjacent side (Site-2′). Distance and contact analyses support a predominantly non-covalent within-cleft mechanism and do not indicate a persistent approach to the literature-reported covalent regime near Cys91. Residue-level profiling over the stabilized sampling window defines a reproducible corridor “contact signature” and reveals within-cavity sub-pose diversity rather than a single rigid bound pose. Mechanistically, competitive docking of the native agonist cGAMP to ExcB-conditioned receptor snapshots yields consistently less favorable docking outcomes in ExcB-conditioned conformations than docking to the native/open receptor; retaining ExcB coordinates does not further penalize cGAMP, supporting a receptor-reshaping (conformational conditioning) component rather than persistent static steric clash. Our findings characterize ExcB as a non-covalent modulator targeting a cryptic pocket within the STING CDN-binding cleft, establishing a structural basis for targeted mutagenesis and structure-activity relationship (SAR) studies. Full article

Antiviral substances are considered emerging contaminants. Once released into the environment, they may affect organisms through complex and often still-unknown mechanisms. This study focuses on a class of antiviral substances with potential use in treating COVID-19 patients, aiming to identify specific structural characteristics that significantly contribute to their ecotoxicity. An empirical approach called quantitative structure–activity relationship (QSAR) was used for this purpose. The study examined 13 antiviral substances: atazanavir, daclatasvir, darunavir, emtricitabine, favipiravir, lopinavir, nirmatrelvir, oseltamivir, remdesivir, ribavirin, ritonavir, and sofosbuvir. The ecotoxicity of these antivirals was assessed using three tests: the Aliivibrio fischeri test, the Chlorella sp. test, and the Pseudomonas putida test. These three microorganisms represent different trophic levels in aquatic and soil ecosystems. Ecotoxicity was expressed as EC₂₀ and EC₅₀, and these values served as the dependent variables in the QSAR models. A large set of numerical descriptors calculated from the molecular structures of the antivirals was used as an independent variable. EC₂₀-based QSAR models offer insight into the effects of antivirals under sub-lethal exposure conditions. The results indicated that sub-lethal exposure in Aliivibrio fischeri was associated with favorable electronic properties and compact structures that promote cellular accumulation, while long-range fragments reduced toxicity. In Chlorella sp., sub-lethal exposure was driven by optimal molecular size, chain length, and specific electronic groups enabling cell penetration and biochemical inhibition. For sub-lethal exposure in P. putida, lipophilicity and reactive group geometry enhanced toxicity, while high short-range polarity mitigated it by limiting membrane permeability. Acute toxicity patterns showed similar trade-offs: strong electronic reactivity increased potency, but steric bulk, long-range polarity, or unfavorable mass distribution frequently restricted bioavailability and reduced toxic effects. Overall, the models demonstrated that antiviral toxicity results from a balance of electronic activity, structural accessibility, and physicochemical constraints, providing a mechanistic basis for predicting the environmental risk of selected antiviral substances. Full article

Two structurally tunable (propyl-3-ol)triphenyltin(IV) (Ph₃SnL₁) and (butyl-4-ol)triphenyltin(IV) (Ph₃SnL₂) compounds were investigated at the human serum transferrin (Tf) molecular interface to resolve how ligand architecture and protein metallation modulate organotin(IV) biocompound stability and lobe-selective binding. Steady-state fluorescence spectroscopy revealed efficient quenching of native Tf emission (λ_ex = 280 nm, 296–310 K, pH 7.4) without significant spectral displacement, indicating the predominant formation of non-fluorescent ground-state complexes. Calculated bimolecular quenching constants (K_q ~10¹² M⁻¹ s⁻¹) exceeded the diffusion-controlled aqueous limit, ruling out a collisional dynamic quenching mechanism and confirming static complexation as the principal origin of fluorescence suppression. Double-log binding analysis revealed moderate affinity (K_a ~10²–10³ M⁻¹) and an approximately single dominant binding event per protein (n ≈ 0.65–0.90). Temperature-dependent van’t Hoff evaluation yielded positive ΔH° and ΔS° values, supporting a spontaneous, entropy-favored association process largely governed by hydrophobic and dispersion-type contributions, consistent with lipophilic organotin(IV) scaffold accommodation. Iron (Fe³⁺) loading of Tf markedly enhanced ligand engagement, especially for Ph₃SnL₁, evidencing that metallation-induced lobe closure reshapes pocket accessibility and local polarity relevant for organotin(IV) binding presentation rather than simply strengthening empirical docking scores. Molecular docking localized the most stable Ph₃SnL₂ poses in the sterically confined, rigid C-lobe, while Ph₃SnL₁ preferentially penetrated the more adaptive N-lobe. ONIOM QM/MM refinement of docking poses confirmed strong interfacial stabilization (ΔE_int ≈ –38 to –62 kcal mol⁻¹) and clarified charge–packing interplay without invoking frontier orbital analysis. The results map multiscale structure–interaction relationships defining lobe preference and complex stability at the transferrin interface. Full article