Search Results (41)

In this work, the regio- and stereochemistry as well as the molecular mechanism of the cycloaddition reaction of nitrones with (E)-3-(methylsulfonyl)-propenoic acid derivatives were analyzed based on ωb97xD/6-311G(d,p) quantum chemical calculations. In light of these data, it is possible to propose selectivity of the analyzed processes, which was not clearly determined in light of previous experimental studies. Furthermore, the mechanism of the process was diagnosed. CDFT descriptors indicate that the reaction is triggered by a nucleophilic attack of the nitrone oxygen atom on the electrophilic carbon atom of (E)-3-(methylsulfonyl)-propenoic acid derivatives. In turn, PES analysis shows that, despite the nucleophilic-electrophilic character of the reactants, the corresponding transition states are only weakly polar and highly synchronous. IRC calculations rule out zwitterionic or biradical intermediates, confirming a single-step mechanism. The in silico ADME and PASS predictions indicate that the resulting isoxazolidines possess promising biological profiles, showing potential modulation of the serotonin system through 5-HT2A and 5-HT2C antagonism and stimulation of serotonin release, with structural features compatible with P450-mediated metabolism. Considering this attractive application potential, a detailed mechanistic investigation of their formation becomes essential for understanding and ultimately controlling the reaction pathways leading to these heterocycles. Full article

We investigated the Diels-Alder cycloaddition of methylcyclopentadiene with conjugated nitroalkenes and examined the influence of solvent polarity and substituent effects on the reaction mechanism. In nonpolar media (toluene), pathways A and C proceed via a pre-reactive molecular complex (MC), two transition states, and a heterocyclic intermediate, whereas pathways B and D follow a single-transition-state route directly to the norbornene product. Moderate increases in solvent polarity (acetone) do not qualitatively alter the energy profiles or mechanistic patterns, whereas highly polar solvents (methanol, acetonitrile, water, nitromethane) induce a fundamental transformation in pathway B, which adopts a stepwise, zwitterionic mechanism. NPA, MEP, and NCI analyses confirm the polar, charge-separated nature of the zwitterionic intermediate, while BET analysis elucidates the sequential electronic reorganization, highlighting early polarization toward the nitro fragment and stepwise formation of the C-C bonds. Substituent effect studies using Hammett σ parameters reveal that electron-withdrawing groups lower activation barriers, whereas electron-donating groups increase them, indicating that electronic effects dominate over steric factors. Overall, the study demonstrates a general, solvent- and substituent-dependent Diels-Alder mechanism, with pathway B proceeding through a polar, highly asynchronous, stepwise route involving a zwitterionic intermediate. Full article

Pyridinium ylides, along with related azaheterocyclic ylides, are widely used in synthetic organic chemistry. However, reactions that yield stable zwitterionic adducts from these ylides remain underexplored. In this work, we demonstrate that the reaction of pyrrole-2,3-diones with in situ-generated pyridine-based azomethine ylides affords stable zwitterionic adducts, which are typically transient species in analogous processes. These betaines are used as key intermediates for the synthesis of cyclopropane-fused pyrroles or pyridine-2,3-diones via thermolysis in chlorobenzene. Full article

Sulfur-containing heterocyclic structures play an important role in modern biotechnology. Their synthesis is made possible by means of the hetero Diels–Alder reaction involving unsaturated sulfur compounds. In the framework of this paper, the molecular mechanism of the cycloaddition reactions between tioanalogs of the butadiene generated in situ with the participation of the Lawesson reagent and the E-2-phenyl-1-nitroethene was evaluated on the basis of the DFT quantum chemical calculations. It was found that the most favored reaction path is realized according to a stepwise mechanism with the participation of the zwitterionic intermediate. To study this further, the molecular mechanism of the deamination process of the primary cycloadducts was also analyzed. It was found that this mechanism is substantially different to the case of other known β-elimination processes and is achieved via a stepwise scheme. In addition to these investigations, the LA catalysis of the deamination process was also explored. Full article

Building on the early investigation by Sidney W. Fox that dry-heated amino acids can spontaneously form microspheres, this research studies the self-organization of glycine and alanine with hydrogen in a liquid system. This study aimed to investigate the spontaneous formation of membraneless, microscale amino acid assemblies under simulated prebiotic hydrothermal conditions, such as hot mineral sources and ponds. Aqueous solutions of glycine and alanine were prepared in a hydrogen-rich mineral buffer and thermally incubated at 75 °C. Phase-contrast microscopy, transmission electron microscopy (TEM), and molecular modeling were employed to analyze the morphology and internal organization of the resulting structures. Microscopy revealed that zwitterionic glycine and alanine spontaneously self-organize into spherical microspheres (~12 µm), in which the charged –NH₃⁺ and –COO⁻ groups orient outward, while the hydrophobic methyl groups of alanine point inward, forming a stabilized internal core. The primary studies were performed with hot mineral water from Rupite, Bulgaria, at 73.4 °C. The resulting osmotic pressure difference Δπ ≈ 2490 Pa, derived from the van’t Hoff equalization. This suggests a chemically asymmetric system capable of sustaining directional water flux and passive molecular enrichment. The zwitterionic nature of glycine and alanine, which possesses both –NH₃⁺ and –COO⁻ groups, supports the formation of microspheres in our experiments. Under conditions with hot mineral water and hydrogen acting as a reducing agent in the primordial atmosphere, these amino acids self-organized into dense interfacial microspheres. These findings support the idea that thermally driven, zwitterion-mediated aggregation of simple amino acids, such as glycine and alanine, with added hydrogen, could generate membraneless, selectively organized microenvironments on the early Earth. Such microspheres may represent a plausible intermediate between dispersed organisms and microspheres. Full article

Background/Objectives: Army Liposome Formulation with QS21 (ALFQ) is a vaccine adjuvant formulation consisting of liposomes that contain saturated zwitterionic and anionic phospholipids, 55 mol% cholesterol, and small molar amounts of monophosphoryl lipid A (MPLA) and QS21 saponin as adjuvants. A unique aspect of ALFQ is that after addition of QS21 to nanoliposomes (<100 nm), the liposomes self-assemble through fusion to form giant (≥1000 nm) unilamellar vesicles (GUVs). The purpose of this study was to introduce and investigate new intermediate structures in the fusion process that we term tethered incomplete microspheres (TIMs), which were discovered by us incidentally as structures that were visible by phase contrast microscopy. Methods: Differential centrifugation; phase contrast microscopy; confocal microscopy of vesicles or TIMs which contain fluorescent chromophores linked to phospholipids or cholesterol; ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis of lipid components of liposomes and TIMs; and dynamic light scattering were all used for the characterization of TIMS. Results and Conclusions: (A) Sizes of TIMs range from overall aggregated structural sizes of ~1 µm to mega sizes of ≥200 µm. (B) Stable TIM structures occur when a fusion process is stopped by depletion of a fusogenic lipid during an evolving fusing of a lipid bilayer membrane. (C) TIMs consist of long-term stable (>2 years), but also metastable, tightly aggregated tear-drop or spherical incomplete GUVs tethered to visible masses of underlying vesicles that are not individually visible. (D) The TIMs and GUVs all contain phospholipid and cholesterol (when present) as bulk lipids. (E) Lyophilized liposomes lacking QS21 saponin, but which still contain MPLA (ALF55lyo), also self-assemble to form GUVs and TIMs. (F) Cholesterol is a required component in nanoliposomes for generation of GUVs and TIMs by addition of QS21. (G) Cholesterol is not required for production of GUVs and TIMs in ALFlyo, but cholesterol greatly reduces and narrows the polydisperse vesicle distribution. Full article

1,3-Diphenylisobenzofuran (DPBF) is a widely used fluorescent probe for singlet oxygen (¹O₂) detection in photodynamic applications. In this work, we present an integrated experimental and computational analysis to describe its spectroscopic, photophysical, and reactive properties in ethanol, DMSO, and DMF. UV-Vis and fluorescence measurements across a wide concentration range show well-resolved S₀ → S₁ electronic transition of a π → π* nature with small red shifts in polar aprotic solvents. Fluorescence lifetimes increase slightly with solvent polarity, showing stabilization of the excited state. The 2D PES and Boltzmann populations analysis indicate two co-existing conformers (C_s and C₂), with C_s being slightly more stable at room temperature. TD-DFT calculations have been performed using several density functionals and the 6-311+G(2d,p) basis set to calculate absorption/emission wavelengths, oscillator strengths, transition dipole moments, and radiative lifetimes. Overall, cam-B3LYP and ωB97X-D provided the best agreement with experiments for the photophysical data across all solvents. The photophysical behavior of DPBF upon interaction with ¹O₂ can be explained by a small-barrier, two-step reaction pathway that goes through a zwitterionic intermediate, resulting in the formation of 2,5-endoperoxide. This work explains the photophysical properties and reactivity of DPBF, therefore providing a solid basis for future studies involving singlet oxygen. Full article

Aggregation of tau protein is a hallmark feature of tauopathies such as Alzheimer’s disease. The microtubule-binding domain of tau plays a crucial role in the tau aggregation process. In this study, we investigated the dual effects of membrane interactions of tau_298–317, a fragment peptide from the microtubule-binding domain, on peptide-induced membrane disruption and membrane-mediated peptide self-assembly. Our results show that neither wild-type tau_298–317 nor its P301L or Ser305-phosphorylated mutants aggregate in the presence of zwitterionic POPC vesicles or cause lipid vesicle leakage, indicating weak peptide–membrane interactions. In contrast, tau_298–317 strongly interacts with negatively charged POPG liposomes, leading to a rapid transition of the peptide conformation from random coils to α-helical intermediate conformation upon membrane adsorption, which may further promote peptide self-association to form oligomers and β-sheet-rich fibrillar structures. Tau_298–317-induced rapid POPG membrane leakage indicates a synergistic process of the peptide self-assembly at the membrane interface and the aggregation-induced membrane disruption. Notably, phosphorylation at Ser305 disrupts favorable electrostatic interactions between the peptide and POPG membrane surface, thus preventing peptide aggregation and membrane leakage. In contrast, the P301L mutation significantly enhances membrane-mediated peptide aggregation and peptide-induced membrane disruption, likely due to alleviation of local conformational constraints and enhancement of local hydrophobicity, which facilitates fast conformational conversion to β-sheet structures. These findings provide mechanistic insights into the molecular mechanisms underlying membrane-mediated aggregation of crucial regions of tau and peptide-induced membrane damage, indicating potential strategies to prevent tau aggregation and membrane rupture by targeting critical electrostatic interactions between membranes and key local regions of tau. Full article

The regioselectivity and the molecular mechanism of the Diels–Alder reactions between N-(2,2,2-trichloroethylidene)carboxamides and dicyclohexylcarbodiimide were explored based on the ωB97xd/6-311G(d) (PCM) calculations. It was found that the reaction course is determined by polar local interactions. It is interesting that the most favored reaction channel is realized not via classical single-step Diels–Alder mechanism, but according to the stepwise scheme with the intervention of the zwitterionic intermediate. The details of the electron density redistribution along the reaction coordinate were explained using the ELF technique. Full article

The phenomena of regio- and stereoselectivity and the molecular mechanism of the [2 + 2] cycloaddition reaction between (E)-2-arylnitroethenes and the ynamine molecular system were analyzed using wb97xd/6-311 + G(d) (PCM) quantumchemical calculations. It was found that, independently of the stepwise nature of the cycloaddition, the full retention of the stereoconfiguration of the nitroalkene can be interpreted and explained. Next, the analysis of the electronic properties of the localized reaction intermediate suggests its possible zwitterionic nature. Additionally, the solvent and the substituent effect on the reaction course were also evaluated. In consequence, the proposed mechanism can be treated as general for some groups of [2 + 2] cycloaddition processes. Lastly, for the model process, the full Bonding Evolution Theory (BET) analysis along the reaction coordinate was performed. It was found that the [2 + 2] cycloaddition reaction between (E)-2-phenylonitroethene and ynamine begins with the formation of two pseudoradical centers at the C2 and C3 atoms. First, a C2-C3 single bond is formed in phase V by combining two pseudoradical centers, while the formation of a second C4-C1 single bond begins at the last, eleventh phase of the reaction path. A BET analysis of intermediate (I) allows it to be classified as a compound with a pseudoradical structure. Next to zwitterions and biradicals, it is evidently new type of intermediate on the path of the [2 + 2] cycloaddition reaction. Full article

Cultural Heritage is a vital socioeconomic driver that must contend with works of art continuously exposed to degradation processes, which are further exacerbated by climate change. Aged coatings, varnishes, and soil can compromise the appearance of artworks, preventing their preservation and valorization. In response, soft matter and colloidal systems, such as nanostructured cleaning fluids (NCFs), have proved to be valuable solutions for safely and effectively cleaning works of art. Here, a novel cleaning system is proposed, for the first time employing microgels of poly(N-isopropylacrylamide) (PNIPAM) with surface chains of oligoethylene glycol methyl ether methacrylate (OEGMA) to favor shear deformation by lubrication. These microgels are loaded with NCFs featuring “green” solvents and different kinds of bio-derived or petroleum-based surfactants (non-ionic, zwitterionic). Rheological characterization of the combined systems highlighted a sharp transition from solid to liquid-like state in the 21–24 °C range when the zwitterionic surfactant dodecyldimethylamine oxide was used; the system displays a solid-like behavior at rest but flows easily at intermediate strains. At slightly higher temperature (>24 °C), an inversion of the G′, G″ values was observed, leading to a system that behaves as a liquid. Such control of rheological behavior is significant for feasible and complete removal of soiled polymer coatings from textured ceramic surfaces, which are difficult to clean with conventional gels, without leaving residues. These results position the PNIPAM-OEGMA microgels as promising cleaning materials for the conservation of Cultural Heritage, with possible applications also in fields where gelled systems are of interest (pharmaceutics, cosmetics, detergency, etc.). Full article

This review probes the recent developments in stereoselective reactions within the area of sulfoxonium ylide chemistry since the early 2000s. An abundance of research has been applied to sulfoxonium ylide chemistry since its emergence in the early 1960s. There has been a continued effort since then with work in traditional areas, such as epoxidation, aziridination and cyclopropanation. Efforts have also been applied in novel areas, such as olefination and insertion reactions, to develop stereoselective methodologies using organocatalysis and transition metal catalysis. The growing research area of interrupted Johnson–Corey–Chaykovsky reactions is also described, whereby unexpected stereoselective cyclopropanation and epoxidation methodologies have been developed. In general, the most observed mechanistic pathway of sulfoxonium ylides is the formal cycloaddition: (2 + 1) (e.g., epoxides, cyclopropanes, aziridines), (3 + 1) (e.g., oxetanes, azetidines), (4 + 1) (e.g., indanones, indolines). This pathway involves the formation of a zwitterionic intermediate through nucleophilic addition of the carbanion to an electrophilic site. An intramolecular cyclization occurs, constructing the cyclic product. Insertion reactions of sulfoxonium ylides to X–H bonds (e.g., X = S, N or P) are also observed, whereby protonation of the carbanion is followed by a nucleophilic addition of X, to form the inserted product. Full article

Nowadays, nucleic acid derivatives capable of modulating gene expression at the RNA level have gained widespread recognition as promising therapeutic agents. A suitable degree of biological stability of oligonucleotide therapeutics is required for in vivo application; this can be most expeditiously achieved by the chemical modification of the internucleotidic phosphate group, which may also affect their cellular uptake, tissue distribution and pharmacokinetics. Our group has previously developed a strategy for the chemical modification of the phosphate group via the Staudinger reaction on a solid phase of the intermediate dinucleoside phosphite triester and a range of, preferably, electron deficient organic azides such as sulfonyl azides during automated solid-phase DNA synthesis according to the conventional β-cyanoethyl phosphoramidite scheme. Polyfluoro compounds are characterized by unique properties that have prompted their extensive application both in industry and in scientific research. We report herein the synthesis and isolation of novel oligodeoxyribonucleotides incorporating internucleotidic perfluoro-1-octanesulfonyl phosphoramidate or 2,2,2-trifluoroethanesulfonyl phosphoramidate groups. In addition, novel oligonucleotide derivatives with fluorinated zwitterionic phosphate mimics were synthesized by a tandem methodology, which involved (a) the introduction of a carboxylic ester group at the internucleotidic position via the Staudinger reaction with methyl 2,2-difluoro-3-azidosulfonylacetate; and (b) treatment with an aliphatic diamine, e.g., 1,1-dimethylethylenediamine or 1,3-diaminopropane. It was further shown that the polyfluoro oligonucleotides obtained were able to form complementary duplexes with either DNA or RNA, which were not significantly differing in stability from the natural counterparts. Long-chain perfluoroalkyl oligonucleotides were taken up into cultured human cells in the absence of a transfection agent. It may be concluded that the polyfluoro oligonucleotides described here can represent a useful platform for designing oligonucleotide therapeutics. Full article

Zwitterionic π-allenyl palladium species are newly developed intermediates. A substrate-controlled step existed in the cycloaddition of zwitterionic π-allenyl palladium species with tropsulfimides or tropones. With the assistance of previously experimental studies, zwitterionic allenyl/propargyl palladium species was provenly found by HRMS. Further DFT calculation studies show that zwitterionic π-allenyl palladium species are generated through the oxidative addition of Pd(0), which can be promoted by Lewis acid like Yb(OTf)₃, and the cycloaddition more likely undergoes through an outer sphere nucleophilic attack. The isomerization is caused by the difference of dissociation energy between the cycloaddition intermediation of tropsulfimides and tropones, forming the substrate-controlled specificity. Full article

The regio- and stereoselectivity and the molecular mechanisms of the [3 + 2] cycloaddition reactions between Syn-propanethial S-oxide and selected conjugated nitroalkenes were explored theoretically in the framework of the Molecular Electron Density Theory. It was found that cycloadditions with the participation of nitroethene as well as its methyl- and chloro-substituted analogs can be realized via a single-step mechanism. On the other hand, [3 + 2] cycloaddition reactions between Syn-propanethial S-oxide and 1,1-dinitroethene can proceed according to a stepwise mechanism with a zwitterionic intermediate. Finally, we evaluated the affinity of model reaction products for several target proteins: cytochrome P450 14α-sterol demethylase CYP51 (RSCB Database PDB ID: 1EA1), metalloproteinase gelatinase B (MMP-9; PDB ID: 4XCT), and the inhibitors of cyclooxygenase COX-1 (PDB:3KK6) and COX-2 (PDB:5KIR). Full article