Search Results (979)

Background/Objectives: The development of specific inhibitors for cyclooxygenase-2 (COX-2) is a challenge for public health. A series of 17 N-phthalimide hybrids was evaluated using a functional M06 meta-GGA hybrid in combination with a polarized 6-311G (d, p) basis set. The top three candidates (6, 10, and 17) were synthesized and evaluated as selective COX-2 inhibitors of PGE-2 using an integrated in silico–in vitro approach. Methods: Molecular docking against COX-2 (PDB 5KIR) and COX-1 (PDB 6Y3C), supported by homology modeling and DFT geometry optimization (B3LYP/6-31G*), revealed that the phthalimide carbonyl groups and the 3,4,5-trimethoxyphenyl or geranyl-derived moieties establish key hydrogen bonds and hydrophobic contacts with Arg120, Tyr355, Tyr385, and Ser530 in the COX-2 active site, conferring predicted selectivity ΔGCOX−2 vs. COX−1 = −1.4 to −2.8 kcal/mol. Results: The compounds complied with Lipinski’s and Veber’s rules and displayed favorable ADMET profiles. In vitro assessment in LPS-stimulated J774A.1 murine macrophages confirmed potent inhibition of PGE₂ production, 3.05 µg/mL, with compound 17 exhibiting the highest efficacy, 97.79 ± 5.02% inhibition at 50 µg/mL, and 10 showing 95.22 ± 6.03% inhibition at 50 µg/mL. Notably, all derivatives maintained >90% cell viability up to 250 µg/mL by resazurin assay and showed no evidence of cytotoxicity or mitosis potential in the tests at 24 h. Conclusions: These results demonstrate that strategic hybridization of phthalimide with natural and synthetic product-derived fragments yields highly potential PGE2 inhibitors. Therefore, compounds 6, 10, and 17 are promising lead candidates for the development of safer anti-inflammatory agents. Full article

Collagen type I has become a practical cornerstone for constructing biologically meaningful barrier interfaces in microfluidic systems. Its fibrillar architecture, native ligand display, and susceptibility to cell-mediated remodeling support epithelial and endothelial polarization, tight junctions, and transport behaviors that are difficult to achieve with purely synthetic barrier interfaces. Recent advances pair these biological strengths with tighter engineering control. For example, ultrathin collagen barriers (tens of micrometers or less) enable faster molecular exchange and short-range signaling; gentle crosslinking and composite designs limit gel compaction and delamination under flow; and patterning/bioprinting introduce alignment, graded porosity, and robust integration into device geometries. Applications now span intestine, vasculature, skin, airway, kidney, and tumor–stroma interfaces, with readouts including transepithelial/transendothelial electrical resistance (TEER), tracer permeability, and image-based quality control of fiber architecture. Persistent constraints include batch variability, long-term mechanical drift, limited standardization of fibrillogenesis conditions, and difficulties scaling fabrication without loss of bioactivity. Priorities include reporting standards for microstructure and residual crosslinker, chips for continuous monitoring, immune-competent co-cultures, and closer collaboration across materials science, microfabrication, computational modelling, and clinical pharmacology. Thus, this review synthesizes the state-of-the-art and offers practical guidance on technological readiness and future directions for using collagen type I as a biological barrier interface in biomimetic microfluidic systems. Full article

Understanding how supercritical CO₂ and water interact with mineral surfaces is essential for predicting the stability and sealing performance of geological storage formations. Yet, the combined effects of mineral surface chemistry and confined pore geometry on interfacial structure and fluid dynamics remain insufficiently resolved at the molecular scale. In this study, molecular dynamics simulations were employed to quantify how methylated SiO₂, hydroxylated SiO₂, and kaolinite regulate CO₂–H₂O interfacial behavior through variations in wettability and electrostatic interactions. The results show a clear hierarchy in water affinity across the three minerals. On methylated SiO₂, the water cluster remains spherical and poorly anchored, with a contact angle of ~140°, consistent with the weakest water–surface Coulomb attractions (only −400 to −1400 kJ/mol). Hydroxylated SiO₂ significantly enhances hydration, forming a cylindrical water layer with a reduced contact angle of ~61.3° and strong surface–water electrostatic binding (~−18,000 to −20,000 kJ/mol). Kaolinite exhibits the highest hydrophilicity, where water forms a continuous bridge between the two walls and the contact angle further decreases to ~24.5°, supported by the strongest mineral–water electrostatic interactions (−23,000 to −25,000 kJ/mol). Meanwhile, CO₂–water attractions remain moderate (typically −2800 to −3500 kJ/mol) but are sufficient to influence CO₂ distribution within the confined domain. These findings collectively reveal that surface functionalization and mineral type govern interfacial morphology, fluid confinement, and electrostatic stabilization in the sequence methylated SiO₂ < hydroxylated SiO₂ < kaolinite. This molecular-level understanding provides mechanistic insight into how mineral wettability controls CO₂ trapping, fluid segregation, and pore-scale sealing behavior in subsurface carbon-storage environments. Full article

Designing the high-performance polyimides (PIs) for the biomimetic structures, which are used in extreme conditions, remains greatly challenging, due to the conflict between processability and thermal stability. Here, we report a series of silicon–alkyne-functionalized diamine-based polyimides that exhibit remarkable processability and thermal stability. The incorporation of bulky siloxy groups disrupts chain packing and increases free volume, enabling excellent solubility in polar solvents, while the rigid fluorene core enhances chain stiffness. DFT calculations confirm twisted molecular geometries (Si bond angle ≈ 103°, dihedral angle ≈ 89°) which weak π–π stacking, while heterogeneous electrostatic potentials enable favorable noncovalent interactions (e.g., C–F···H–C), promoting solvent diffusion. After thermal curing, the obtained product shows a high decomposition temperature (T_d5% = 560 °C), char yield of 72.0% at 800 °C, and glass transition temperature (T_g) of 354.6 °C. Meanwhile, locally planar fluorene units retain inherent thermal stabilization benefits through constrained rotational mobility. These results demonstrate a spatially decoupled siloxy–alkyne design that synergistically enhances molecular flexibility, disorder, and electronic stability, offering a molecular strategy for tailoring PI-based matrices to meet the demands of emerging biomimetic architectures and other high-performance composites operating under severe thermal loads. Full article

The accurate determination of bond lengths is fundamental to understanding molecular geometry and the physicochemical behavior of chemical compounds. However, obtaining these measurements is often challenging, as both experimental techniques and advanced quantum-chemical methods are complex, computationally demanding, and costly to apply across diverse molecular systems. In this work, we present a novel graph-theoretical model for predicting bond lengths in flavonoid molecules based on molecular descriptors derived from atomic and topological parameters. By integrating atomic electronegativity with graph-based descriptors, such as the weighted second-order neighborhood, the proposed model predicts the bond lengths of luteolin with a coefficient of determination of $R^2=0.990$. This approach offers a computationally efficient and highly accurate alternative to conventional experimental and theoretical methods, providing a practical framework for bond length estimation when experimental data are unavailable. Full article

Background/Objectives: Leishmaniasis constitutes one of the most fatal parasitic diseases globally, adversely impacting the health of individuals residing in both intertropical and temperate zones. In these geographical areas, the administration of treatment is often inconsistent and largely ineffective with the available pharmaceuticals, as these exhibit more pronounced side effects than the therapeutic advantages they purport to provide. Methods: Consequently, the current investigation seeks to engage in molecular modeling of novel pharmacological candidates incorporating 1,2,3 disubstituted triazole moieties, coordinated with Cu^II metal centers, in pursuit of promising bioactive properties. Results: Two complexes were prepared and X-ray analysis revealed a comparable structural configuration surrounding the copper (II) atom. The planar square coordination geometry was elucidated through the assessment of the ${\tau }_4=0$ (tau four) parameters. The comprehensive characterization encompasses HRMS-ESI (+), NMR, elemental analyses, mid-infrared, and UV-vis spectroscopic techniques. Time-dependent density functional theory (TD-DFT) analyses will substantiate the findings obtained through UV-vis spectroscopy. Crucially, the biological assays against Leishmania (L.) amazonensis revealed that Complex 1 exhibited outstanding potency against the intracellular amastigote form, demonstrating a half-maximal inhibitory concentration (IC₅₀) of 0.4 µM. This activity was 6-fold higher than that of amphotericin B (IC₅₀ = 2.5 µM) and 33-fold higher than pentamidine (IC₅₀ = 13.3 µM). Furthermore, Complex 1 showed a promising selectivity index (SI = 9.7) against amastigotes, surpassing the reference drugs and meeting the criteria for a lead compound. While less active on promastigotes, both complexes demonstrated high stability in DMSO solution, a prerequisite for biological testing. Conclusions: These results unequivocally identify Complex 1 as a highly promising candidate for the development of new antileishmanial therapies, warranting further in vivo studies. Full article

Coordination polymers (CPs) are garnering attention in the field of medicine day by day. The goal is to develop a CP with biosafe and environment-friendly characteristics. Herein, we report two such novel 3D coordination polymers of zinc-inosine-5′-monophosphate (Zn-IMP) and bpe/azpy (as linkers) which were engineered as metal–organic frameworks that can be used as drug carriers for hydroxyurea (HU). We employed SCXRD, PXRD, solid-state CD, FTIR and TGA for crystal structure characterizations; the results achieved 3D coordination polymers which contain a P2₁ space group with chiral distorted tetrahedral geometry. Solution phase studies like UV–vis and CD were carried out to understand mechanistic pathways for interaction and chirality, respectively. We have also performed computational studies to evaluate the drug delivery capacity of both 3D CPs. Molecular docking and multi-pH molecular dynamics (MD) quantify that HU binds more strongly with CP−1 (ΔG =−10.87 ± 0.12) as compared to CP−2 (ΔG = −7.59 ± 0.26 kcal·mol⁻¹), at normal and basic pH. MD simulation analysis indicated that a more compact and rigid cavity is observed by CP−1 as compared to CP−2 at physiological pH. Across acidic pH, for CP−1 the ligand RMSD increases markedly and U becomes slightly less negative, which indicated partial loss of contacts, thus releasing drugs in a tumor-like environment more easily. These result showed that CP−1 offers stronger binding, higher structural stability and a more pronounced pH-responsive release profile than CP−2, making CP-1 more promising candidate for targeted HU drug delivery, while CP−2 may serve as a weaker-binding, faster-release complement. Full article

Understanding the atomic-level behavior of photocatalysts under hydrated conditions is essential for improving hydrogen production efficiency. In this work, density functional theory calculations and classical all-atom molecular dynamics simulations were performed to investigate the intra- and intermolecular interactions of rod- and cluster-shaped cadmium sulfide in the presence of implicit and explicit water, respectively. The density functional theory optimized geometries, reduced density gradient, noncovalent interaction, critical point, and molecular electrostatic potential maps were examined using the LC-ωPBE functional with the LANL2DZ basis set and the IEFPCM implicit solvation model, while explicit hydration was modeled via classical all-atom molecular dynamics simulations by obtaining molecular snapshots and radial distribution functions. Density functional theory results revealed that rod-shaped cadmium sulfide exhibits stronger directional bonding and higher electronic localization compared to cluster-shaped cadmium sulfide, while classical all-atom molecular dynamics simulations showed that water molecules preferentially interact with surface S atoms of cadmium sulfide sites. This atomistic insight clarifies how morphology and hydration jointly modulate cadmium sulfide electronic structure and reactivity, providing guidance for the rational design of efficient cadmium sulfide-based photocatalysts for solar-driven water splitting. Full article

Novel copper(II) coordination compounds with hemiaminal N,O-donor ligands were obtained and synthesized in a one-pot reaction from three appropriate substrates (aldehyde, amine, and copper(II) chloride) in methanol. A dinuclear complex with a [Cu₂Cl₂(hemiaminal)₂(amine)₂] coordination mode was obtained. The complex consists of two five-coordinated central Cu(II) cations with square pyramidal geometry and C_i molecular symmetry. The hemiaminal oxygen atom forms a bridge between the two metallic centers, and that coordination bond is a factor stabilizing these hemiaminal moieties, generally regarded as unstable intermediates. We analyzed the energetic and physicochemical properties of the [Cu₂Cl₂(hemiaminal)₂(amine)₂] complex using density functional theory (DFT). First of all, we predicted the geometrical parameters, molecular electrostatic potential, HOMO and LUMO energies, and reactivity indices to indicate the free radical scavenging capacity. Based on the topological analysis of charge densities, we also characterized the properties of hydrogen bonds. Moreover, the antimicrobial properties of the complex were investigated, and it exhibited the highest activity against Gram-positive bacteria and Candida albicans. Full article

Acrolein, a ubiquitous environmental pollutant, is also formed endogenously as a metabolite under oxidative stress conditions. Its adduct to cytosine, 3,N⁴-α-hydroxypropanocytosine (HPC), has recently been shown to be an in vitro substrate for the AlkB dioxygenase. Using a set of indicator plasmids modified with acrolein, we provide evidence that HPC is a mutagenic non-instructional lesion that predominantly induces C→A transversion, and to a lesser extent C→T and C→G base substitutions. HPC is efficiently repaired in vivo by AlkB, even without induction of the adaptive response. However, the mutation frequency did not differ between the wild-type and AlkA-deficient strains, and AlkA glycosylase fails to excise in vitro the acrolein-modified cytosine from the T₂₂(HPC)₃ oligodeoxynucleotide, both indicating that HPC is not a substrate for AlkA. Based on molecular modeling, we further examined the potential differences in the hydrolytic suspensibility of a known AlkA substrate, the acrolein adduct to adenine (HPA), and the cytosine adduct (HPC) at the glycosylase active site. Analysis of both structural and electrochemical properties indicates that, despite an identical type of modification within an equivalent chemical context, including comparable geometry and topology, the glycosidic bond in HPC is considerably less susceptible to hydrolysis than that in HPA. Full article

Ester-based lubricants have been widely used owing to their excellent overall performance. In this study, the quantitative structure–property relationship (QSPR) approach was combined with molecular descriptors, a genetic algorithm (GA), and an artificial neural network (ANN) to systematically predict the key properties—kinematic viscosity at 40 °C and 100 °C, viscosity index, pour point, and flash point—of 64 diester-based lubricants. Quantum chemical calculations were first performed to obtain the equilibrium geometries and electronic information of the molecules. Geometry optimizations and frequency analyses were carried out using the Gaussian 16 software at the B3LYP/6-31G (d, p) level, providing a reliable foundation for molecular descriptor computation. Subsequently, topological, geometrical, and electronic descriptors were calculated using the RDKit toolkit, and the optimal feature subsets were selected by GA and used as ANN inputs for property prediction. The results showed that the ANN models exhibited good performance in predicting viscosity and flash point, with R² values of 0.9455 and 0.8835, respectively, indicating that the ANN effectively captured the nonlinear relationships between molecular structure and physicochemical properties. In contrast, the prediction accuracy for pour point was relatively lower (R² = 0.6155), suggesting that it is influenced by complex molecular packing and crystallization behaviors at low temperatures. Overall, the study demonstrates the feasibility of integrating quantum chemical calculations with the QSPR–ANN framework for lubricant property prediction, providing a theoretical basis and data-driven tool for molecular design and performance optimization of ester-based lubricants. Full article

The aim of this study was to investigate the molecular interactions of heparin, diclofenac, and their supramolecular complexes with cyclooxygenase enzymes (COX-1 and COX-2) using computational docking techniques. Diclofenac is a widely used nonsteroidal anti-inflammatory drug (NSAID) that inhibits COX isoforms, whereas heparin is a polyanionic glycosaminoglycan with established anticoagulant and emerging anti-inflammatory properties. Supramolecular association between these agents may modulate their physicochemical behavior and target engagement. Molecular modeling, dual-drug docking, and molecular dynamics (MD) simulations were employed to characterize the interactions of heparin, diclofenac, and pre-formed heparin–diclofenac complexes with COX-1 and COX-2. Geometry optimization and lipophilicity (logP) estimates were obtained using HyperChem, while protein–ligand docking was performed in HEX using crystallographic COX structures from the Protein Data Bank. Docking poses were analyzed in Chimera, and selected complexes were refined through short MD simulations. Pre-formed heparin–diclofenac assemblies exhibited markedly enhanced docking scores toward both COX isoforms compared with single ligands. Binding orientation strongly influenced affinity: for COX-1, the heparin–diclofenac configuration yielded the most favorable interaction, whereas for COX-2 the diclofenac–heparin configuration was preferred. Both assemblies adopted binding modes distinct from free diclofenac, suggesting cooperative electrostatic and hydrophobic contacts at the enzyme surface. Supramolecular complexation also altered calculated logP values relative to the individual compounds. MD simulations supported the relative stability of the top-ranked complex–COX assemblies. These findings indicate that heparin–diclofenac assemblies may enhance and reorganize predicted COX interactions in a configuration-dependent manner and illustrate the utility of dual-drug docking for modeling potential synergistic effects. Such insights may inform the design of localized or topical formulations, potentially incorporating non-anticoagulant heparin derivatives, to achieve effective COX inhibition with reduced systemic exposure. However, the results rely on simplified heparin fragments, legacy docking tools, and short MD simulations, and should therefore be interpreted qualitatively. Experimental studies will be essential to confirm whether such supramolecular assemblies form under physiological conditions and whether they influence COX inhibition in vivo. Full article

Surface-enhanced Raman scattering (SERS) is a highly sensitive analytical technique capable of single-molecule detection, yet its performance strongly depends on the underlying plasmonic architecture. In this study, we developed a robust SERS platform based on long-range–ordered bullseye plasmonic nano-gratings with tunable period and filling fraction, fabricated via electron beam lithography and reactive ion etching and uniformly coated with a thin gold film. These concentric nanostructures support efficient surface plasmon resonance and radial SPP focusing, enabling intense electromagnetic field enhancement across the substrate. Using this platform, we achieved quantitative detection of Rhodamine 6G with enhancement factors of ${10}^5$. Notably, our results reveal a previously unrecognized mechanistic insight: the geometric configuration producing the strongest local electric fields does not yield the highest SERS enhancement, due to misalignment between the dominant field orientation and the molecular polarizability tensor. This finding explains the non-monotonic dependence of SERS performance on grating geometry and introduces a new design principle in which both field strength and field–molecule alignment must be co-optimized. Overall, this work provides a mechanistic framework for rationally engineering plasmonic substrates for sensitive and quantitative molecular detection. Full article

Hydrogen pipeline compression is essential for H₂ transportation, with low molecular mass limiting achievable pressure ratios. Existing meanline-based studies offer little guidance on 3D-geometry generation, while existing CFD analyses provide limited insight into secondary flows, loss mechanisms, and off-design behavior. An in-house tool combining meanline, streamline-curvature, and genetic algorithms generates CAD-ready geometries, analyzed with steady 3D CFD from surge to choke. In the absence of H₂ experimental data, validation on an air compressor showed CFD errors of 1% in pressure ratio and 2% in isentropic efficiency. Simulations of the H₂ compressor reveal that tip-leakage vortices dominate rotor-exit nonuniformity and mixing losses. Two potential stall triggers are identified: (1) incidence-induced separation at the leading-edge hub corner; (2) vaneless diffuser rotating stall, as hub separation tendencies seem connected to reduced static-pressure recovery. However, a deeper characterization would require advanced unsteady schemes. At choke onset, the incidence reaches −10°, and the relative Mach number at the leading-edge tip is 0.63, indicating a subsonic negative-incidence stall rather than sonic choking. A meanline loss breakdown analysis corroborates CFD by showing that mixing losses and skin friction prevail. Design-improvement areas have been identified to enhance the performance of hydrogen compressors for future energy systems. Full article

Chitosan oligosaccharides (COSs) with defined degrees of polymerization (DP) exhibit distinct bioactivities with promising applications in food, pharmaceutical, and agricultural industries. However, the specific and sustainable production of COSs remains challenging due to the broad product distribution of wild-type chitosanases and the difficulties in enzyme recovery and reuse. In this study, we employed rational design to engineer a GH46 chitosanase (CsnB) from Bacillus sp. BY01 for chitobiose production. Through homology modeling and molecular docking analysis, 15 mutants were designed by targeting key residues structurally critical for substrate stabilization, product release, and active-site geometry in the substrate-binding subsites. The D78Y mutant exhibited exclusive specificity for chitobiose, demonstrating a specific activity of 102.4 U/mg and yielding chitobiose with a purity exceeding 98%, thereby surpassing the previously reported enzymes for chitobiose production. To address the challenges of enzyme stability, purification costs, and product separation, we developed a ReELP system by integrating elastin-like polypeptides (ELPs) with a ReverseCatcher/ReverseTag peptide pair. This system enabled one-step purification and co-immobilization of CsnB-D78Y directly from cell lysate onto biomimetic silica nanoparticles, achieving 96.8% immobilization efficiency and 90.7% activity recovery. The immobilized enzyme exhibited enhanced thermal and pH stability, retaining approximately 50% activity after 12 h at 40 °C compared to only 5.7% for the free enzyme. In reusability assays, the immobilized CsnB-D78Y maintained efficient chitobiose production over 5 consecutive cycles. This work provides a green and cost-effective strategy for the specific and sustainable production of chitobiose, offering new insights into enzyme engineering and immobilization for industrial COS production. Full article