Search Results (607)

In this work, the structures of the isolated anion and anhydrous and monohydrated sodium salts of alizarin red S (ARS) have been theoretically investigated within the density functional theory framework (B3LYP/6-311++G** calculations). The combination of calculations with the scaled quantum mechanics force field (SQMFF) methodology has allowed the assignment of the experimental infrared spectrum of ARS in the solid phase and the determination of the corresponding force constants. The structural analysis also included the investigation of the NMR and UV-visible spectra of the compound in solution in light of the undertaken quantum chemical calculations, the obtained theoretical data being in good agreement with the corresponding experimental ones. The impact of the presence of the Na⁺ counterion and hydration water on the properties of the organic ARS⁻ fragment was evaluated. Atoms in molecules theory (AIM) analysis was also undertaken to obtain further details on the electronic structure of the investigated species, and the HOMO-LUMO gap was determined to evaluate their relative reactivity. Globally, the results obtained in this work extend the available information on alizarin red S and may also be used for the fast identification of the three studied species of the compound investigated (anhydrous and monohydrated sodium salts and isolated anion). Full article

The pharmaceutical industry faces significant challenges when promising drug candidates fail during development due to suboptimal ADME (absorption, distribution, metabolism, excretion) properties or toxicity concerns. Natural compounds are subject to the same pharmacokinetic considerations. In silico approaches offer a compelling advantage—they eliminate the need for physical samples and laboratory facilities, while providing rapid and cost-effective alternatives to expensive and time-consuming experimental testing. Computational methods can often effectively address common challenges associated with natural compounds, such as chemical instability and poor solubility. Through a review of the relevant scientific literature, we present a comprehensive analysis of in silico methods and tools used for ADME prediction, specifically examining their application to natural compounds. Whereas we focus on identifying the predominant computational approaches applicable to natural compounds, these tools were developed for conventional drug discovery and are of general use. We examine an array of computational approaches for evaluating natural compounds, including fundamental methods like quantum mechanics calculations, molecular docking, and pharmacophore modeling, as well as more complex techniques such as QSAR analysis, molecular dynamics simulations, and PBPK modeling. Full article

Fibrate pharmaceuticals (fibrates), as a widespread class of emerging contaminants, pose potential risks to both ecological systems and human health. The photocatalytic system based on nitrogen (N) and fluorine (F) co-doped TiO₂ nanotube arrays (NF-TNAs) provides a renewable solution for fibrate pharmaceutical removal from water, powered by inexhaustible sunlight. In this study, the degradation of two typical fibrates, i.e., bezafibrate (BZF) and ciprofibrate (CPF), under simulated sunlight irradiation through NF-TNAs were investigated. The photocatalytic degradation of BZF/CPF was achieved through combined radical and non-radical oxidation processes, while the generation and reaction mechanisms of associated reactive oxygen species (ROS) were examined. Electron paramagnetic resonance detection and quenching tests confirmed the existence of h⁺, •OH, O₂^•−, and ¹O₂, with O₂^•− playing the predominant role. The transformation products (TPs) of BZF/CPF were identified through high-resolution mass spectrometry analysis combined with quantum chemical calculations to elucidate the degradation pathways. The influence of co-existing ions and typical natural organic matters (NOM) on BZF/CPF degradation were also tested. Eventually, the ecological risk of BZF/CPF transformation products was assessed through quantitative structure–activity relationship (QSAR) modeling, and the results showed that the proposed photocatalytic system can largely alleviate fibrate toxicity. Full article

The development of novel platinum-based anticancer agents remains a critical objective in medicinal inorganic chemistry, particularly in light of resistance and toxicity limitations associated with cisplatin. In this study, the synthesis, structural characterization, quantum chemical analysis, and cytotoxic evaluation of four new acetylplatinum(II) complexes (cis-[Pt(COMe)₂(PASO₂)₂], cis-[Pt(COMe)₂(DAPTA)₂], trans-[Pt(COMe)Cl(DAPTA)₂], and trans-[Pt(COMe)Cl(PASO₂)]: 1–4, respectively) bearing cage phosphine ligands PASO₂ (2-thia-1,3,5-triaza-phosphaadamantane 2,2-dioxide) and DAPTA (3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane) are presented. The coordination geometries and NMR spectral features of the cis/trans isomers were elucidated through multinuclear NMR and DFT calculations at the B3LYP/6-311++G(d,p)/LanL2DZ level, with strong agreement between experimental and theoretical data. Quantum Theory of Atoms in Molecules (QTAIM) analysis was applied to investigate bonding interactions and assess the covalent character of Pt–ligand bonds. Cytotoxicity was evaluated against five human cancer cell lines. The PASO₂-containing complex in cis-configuration, 1, demonstrated superior activity against thyroid (8505C) and head and neck (A253) cancer cells, with potency surpassing that of cisplatin. The DAPTA complex 2 showed enhanced activity toward ovarian (A2780) cancer cells. These findings highlight the influence of ligand structure and isomerism on biological activity, supporting the rational design of phosphine-based Pt(II) anticancer drugs. Full article

A novel interfacial coating agent was developed by modifying silicone oil with polycyclic aromatic hydrocarbons (PAHs) to enhance the insulation performance of HVDC cable accessories. This study investigates the effects of corona and hot–cold cycle aging on the DC breakdown characteristics of the Cross-Linked Poly Ethylene and Ethylene Propylene Diene Monomer (XLPE/EPDM) interface. Interfacial breakdown tests, infrared spectroscopy, and a microstructural analysis were employed to investigate aging mechanisms. The results show that PAH-modified silicone oil significantly increases the breakdown voltage, with 2,4-dihydroxybenzophenone (C₁₃H₁₀O₃) identified as the optimal additive via quantum chemical calculations (QCCs). Even after aging, the modified interface maintains its superior performance, confirming the long-term reliability of the coating. Full article

A modified activated carbon (AC) was developed by modifying with poly(diallyldimethylammonium) chloride (PDADMAC) to enhance its adsorption performance for water treatment applications. Different PDADMAC concentrations were explored and evaluated using methyl red as a model contaminant, with 8 w/v% PDADMAC yielding the best adsorption performance. The kinetics data were well described by the pseudo-first-order equation and homogeneous surface diffusion model. The Freundlich isotherm fit the equilibrium data well, indicating multilayer adsorption and diverse interaction types. The removal efficiency remained similar across a pH range of 5–9 and in the presence of background inorganic (NaCl)/organic compounds (sodium acetate) at different concentrations. Rapid small-scale column tests were performed to simulate continuous flow conditions, and the PDADMAC-modified AC effectively delayed the breakthrough of the contaminant compared to raw AC. Regeneration experiments showed that 0.1 M NaOH with 70% methanol effectively restored the adsorption capacity, retaining 80% of the initial efficiency after five cycles. Quantum chemical analysis revealed that non-covalent interactions, including electrostatic and Van der Waals forces, governed the adsorption mechanism. Overall, the results of this study prove that PDADMAC-AC shows great potential for enhanced organic contaminant removal in water treatment systems. Full article

[1,4,7,10-Tetraazacyclododecano-κ⁴N^1,4,7,10(3-)]silicon(IV) chloride was synthesized from 1,4,7,10-tetraazacyclododecane (cyclen), n-butyl lithium, and silicon tetrachloride. The crystal structure analysis reveals that this cationic compound is a dimer in the solid state with pentacoordinate silicon atoms. The compound was characterized by melting point, IR, and NMR spectroscopy. The quantum chemical analysis shows that this compound might be an interesting precursor to generate a mononuclear silicon (IV) complex with unusual reactivity due to nearly planar tetracoordinate coordination geometry at the silicon atom. Full article

Vibrational analysis of peptides in solution and the theoretical determination of the effects of the microenvironment on infrared and Raman spectra are of key importance in many fields of chemical interest. In this work, we present a computational study combining static quantum mechanical calculations with ab initio molecular dynamics simulations to investigate the vibrational behavior of three peptide models in both the gas phase and in explicit water, under non-periodic boundary conditions. The vibrational spectra of the main amide bands, namely amide I-III and A, were analyzed using a time–frequency approach based on the wavelet transform, which allows the resolution of transient frequency shifts and mode couplings along the trajectories. This combined approach enabled us to perform a time-resolved vibrational analysis revealing how vibrational frequencies, especially of the C=O and N–H stretching modes, evolve over time due to dynamical microsolvation. These fluctuations modulate vibrational couplings and lead to spectral broadening and frequency shifts that correlate with the local structuring of the solvent. In conclusion, our results highlight how the proposed protocol allows for the direct connection between vibrational modes and local structural changes, providing a link from the spectroscopic observable to the structure, the peptide backbone, and its microenvironment. Full article

This study focuses on exploring potential inhibitors of the Marburg virus interferon inhibitory domain protein (MARV-VP35), which is responsible for immune evasion and immunosuppression during viral manifestation. A combination of in silico techniques was applied, including structure-based pharmacophore virtual screening, molecular docking, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis, molecular dynamics (MD), and molecular stability assessment of the identified hits. The docking scores of the 14 selected ligands ranged between −6.88 kcal/mol and −5.28 kcal/mol, the latter being comparable to the control ligand. ADMET and drug likeness evaluation identified Mol_01 and Mol_09 as the most promising candidates, both demonstrating good predicted antiviral activity against viral targets. Density functional theory (DFT) calculations, along with relevant quantum chemical descriptors, correlated well with the docking score hierarchy, and molecular electrostatic potential (MEP) mapping confirmed favorable electronic distributions supporting the docking orientation. Molecular dynamics simulations further validated complex stability, with consistent root mean square deviation (RMSD), root mean square fluctuation (RMSF), and secondary structure element (SSE) profiles. These findings support Mol_01 and Mol_09 as viable candidates for experimental validation. Full article

This study presents a biomonitoring study of surface waters in the Krynka River basin, encompassing three major regional reservoirs: Khanzhenkovskoe, Olkhovskoe, and Zuyevskoe. These water bodies face significant anthropogenic pressure from mining effluents, industrial discharges, and domestic wastewater. Key pollutants identified are surfactants (SAAs), sulfates, phenols, chlorides, and manganese, with chemical oxygen demand (COD) exceeding regulatory limits. The research was conducted in September 2024. Based on the Specific Combinatorial Water Pollution Index, surface waters in the studied objects can be characterized as slightly polluted. To assess the negative impact of the identified pollutants on hydrobionts, the species composition of phytoplankton of the studied water bodies was analyzed. In the Olkhovskoe Reservoir and Olkhovaya River, cyanobacterial blooms (Oscillatoria agardhii G.) were observed, altering biodiversity in the Krynka River and Zuyevskoe Reservoir. Phytoplankton genera Synedra, Amphiprora, and Navicula—established bioindicators of aquatic ecosystem health—were dominant in Khanzhenkovskoe Reservoir, signaling nutrient enrichment and organic pollution. Changes in the species composition and structure of phytoplankton in the Krynka River, its tributaries and reservoirs, indicate a change in the level of saprobic water bodies from β to α-mesosaprobic, which indicates both the general level of surface water pollution and the accumulation of pollutants along the course of the river. The paper presents the results of fluorimetric analysis of photosynthetic activity of natural phytoplankton cells and demonstrates the possibility of using fluorescence induction curves for regular monitoring measurements. Fluorescence parameters indicate a general deterioration of photosynthetic activity of natural phytoplankton. The growth of Oscillatoria agardhii in the waters of the Olkhovskoe Reservoir and of green microalgae in the Zuevskoe Reservoir led to an increase in the fluorescence quantum yield (F_v/F_m) and the total photosynthetic activity index (PI), which makes it possible to use these parameters as indicator parameters reflecting the intensity of “blooming” of various phytoplankton species. Full article

Marine organism-associated microbes are an important source of structurally diverse and biologically active secondary metabolites exhibiting antimicrobial, anticancer, and anti-inflammatory activities. In this study, we investigated Penicillium brevicompactum MSW10-1, isolated from Hydractinia echinata, a marine invertebrate adapted to extreme intertidal and subtidal environments with variable temperature, salinity, and oxygen conditions. Through a combination of LC/MS-guided chemical analysis and chromatographic purification, eight secondary metabolites were isolated, including brevicolactones A (1) and B (2). The absolute chemical structures of 1 and 2 were determined based on NMR spectroscopic experiments, HR-ESIMS data, and quantum chemical ECD calculations. The isolated compounds (1–8) were evaluated for their ability to inhibit hepatic lipogenesis, a key process in lipid metabolism that is dysregulated in metabolic-dysfunction-associated steatotic liver disease. Furthermore, the inhibitory effects of the isolated compounds on lipid accumulation were further evaluated in primary mouse hepatocytes, using Oil Red O staining. These findings suggested that the isolated compounds may serve as promising candidates for the treatment of metabolic liver diseases associated with lipid dysregulation. Full article

The rotational spectra of xanthene and its oxidation product xanthone were investigated by combining quantum chemical calculations with Fourier transform microwave spectroscopy in a jet-cooled environment. Xanthone was unexpectedly generated in the experiment when water was present in the reservoir of xanthene leading to the total disappearance of xanthene after few hours. Structurally, xanthone shows a near planar disposition, whereas xanthene exhibits a non-planar geometry with both benzene rings twisted out of the molecular plane. This geometry enables an inversion motion between two equivalent conformers, giving rise to a splitting in the ground vibrational state. A two-state analysis of the vibration–rotation interaction for the $v=0$ and $v=1$ states gives an energy separation between these states (inversion splitting) of $\Delta E_{01}=4689.7095\left(10\right)\mathrm{MHz}$. This large-amplitude motion leads to vibration–rotation coupling of energy levels. A symmetric double-minimum inversion potential function was determined, resulting in a barrier of about 45 cm⁻¹ in good agreement with that obtained by DFT quantum chemical calculations. Full article

A series of new isatin hydrazones bearing phosphorus-containing moiety was synthesized through a simple, high-yield and easy work-up reaction of phosphine oxide (Phosenazide) or phosphinate (2-chloroethyl (4-(dimethylamino)phenyl)(2-hydrazinyl-2-oxoethyl)phosphinate, CAPAH) hydrazides with aryl-substituted isatins. The ³¹P NMR technique showed that, in most cases, out of 12 examples in solution, the ratio of the two spatial isomers varied from 1:1 to 1:3. Quantum chemical calculations confirmed the predominance of Z,syn form both in the gas phase and in solution. According to X-ray analysis data in crystals, they exist only in Z,syn form too. Most of the phosphine oxide derivatives and 5-methoxy- and 5-bromoaryl phosphinate analogs exhibit anti-aggregant activity at the level of acetylsalicylic acid but inhibit platelet activation processes more effectively. The 5-chloro type phosphinate derivative exhibits anti-aggregant properties more effectively than acetylsalicylic acid under the conditions of the tissue factor (TF)-activated thromboelastography (TEG) model, the ex vivo thrombosis model. Thus, all the obtained results can become the basis for future pharmaceutical developments to create effective anti-aggregation drugs with broad antithrombotic potential. Full article

Terpenoids are the most structurally diverse class of natural products (NPs). Despite their abundance, the functional diversity of bacterial terpene synthases (TPSs), particularly from Streptomyces species, remains largely unexplored. In this study, fourteen Streptomyces strains were subjected to genome sequencing and bioinformatic analysis to systematically mine class I TPSs. A total of forty-eight TPSs were identified and categorized through phylogenetic analysis, and five representative TPSs distantly related to known TPSs were selected for functional investigation. Biochemical assays revealed that TAC28_6116 is a sesquiterpene synthase producing thujopsan-2β-ol (1) and thujopsene (2), marking the first report of thujopsan-2β-ol production from a bacterial source. TAC49_7078 is a diterpene synthase responsible for the formation of ent-phomacta-1(15),3,7-triene (3). Notably, TAC43_2999 was identified as a novel sesterterpene synthase that produced compound 5 in vitro, while the generation of a previously undescribed compound 6, sestermalaysiene, was exclusively detected during in vivo fermentation using the engineered Escherichia coli chassis optimized for terpenoid biosynthesis. Structural elucidation of sestermalaysiene was supported by nuclear magnetic resonance (NMR) analysis and quantum chemical calculations. Its formation might proceed via a rare [4 + 2] cycloaddition mechanism. Overall, this work expands our knowledge of the catalytic diversity of bacterial TPSs and offers promising biocatalysts for terpenoid engineering and discovery. Full article

This study investigates the structural and energetic properties of hydrogen-bonded complexes between indole and a range of aliphatic, cyclic, and aromatic ketones using a combined vibrational spectroscopic and quantum-chemical approach. FTIR measurements in CCl₄ revealed redshifts in the N-H stretching vibration of indole upon complexation, with formation constants (K_a) ranging from 0.3 to 6.6 M⁻¹. Cyclohexanone displayed the strongest binding, while benzophenone exhibited the weakest interaction. Quantum-chemical calculations, employing CREST and MMFF94 conformational sampling, along with M06-2X/6-311++G(d,p) optimizations, confirmed the formation of hydrogen bonds and additional weak interactions that govern the stability of the complex. QTAIM analysis revealed moderate closed-shell hydrogen bonds with electron densities at the bond critical points (ρ) ranging from 0.010 to 0.019 a.u. and potential energy densities (V) from −18.4 to −36.4 kJ mol⁻¹. Multivariate regression analysis established strong correlations (R² = 0.928 and 0.957) between experimental binding constants and theoretical descriptors, including binding energy, NBO charge on oxygen atom, ionization potential, and electrophilicity index, highlighting the interplay between geometric, electronic, and global reactivity factors. This comprehensive study underlines the predictive power of spectroscopic and quantum descriptors for assessing hydrogen bonding in biologically relevant systems. Full article