Search Results (136)

Ergothioneine is a potent non-toxic and very stable antioxidant which is synthesized by fungi, algae, and bacteria but not animals or higher plants. Ergothioneine has been widely used in cosmetics; dietary supplements; and medicine to treat diabetes, cancer, as well as cardiovascular, neurodegenerative, and liver diseases. Ergothioneine presents two tautomeric forms: thione, the majoritarian and more stable form (ERGO), and thiol (ERGT). Ergothioneine cannot cross cell membranes, and human cells rely on a specific transporter, OCTN1, to transport ingested ERGO to different parts of the body. Ergothioneine is very hydrophilic, and it is supposed to act at the water level but not at the membrane one. In this work, I studied the interaction of ERGO and ERGT with a complex biomembrane using molecular dynamics (MD). MD suggests that ERGO, but not ERGT, inserts spontaneously into the membrane interphase and can move from the membrane interphase to the water phase and vice versa, and no oligomerization was observed. Furthermore, ERGO, when inserted in the membrane, does not alter the hydrocarbon chain order. Therefore, ERGO (the thione form of ergothioneine), but not ERGT (the thiol form), might act at both the water and membrane interphase levels. Full article

Background/Objectives: Tegoprazan (TPZ) is a potassium-competitive acid blocker (P-CAB) used to treat conditions such as gastroesophageal reflux disease, peptic ulcer, and Helicobacter pylori infection. It exists in three solid forms: amorphous, Polymorph A, and Polymorph B. This study investigates the molecular basis of polymorph selection, focusing on conformational bias and solvent-mediated phase transformations (SMPTs). Methods: The conformational energy landscapes of two TPZ tautomers were constructed using relaxed torsion scans with the OPLS4 force field and validated by nuclear Overhauser effect (NOE)-based nuclear magnetic resonance (NMR). Hydrogen-bonded dimers were analyzed using DFT-D. Powder X-ray diffraction (PXRD), differential scanning calorimetry (DSC), solubility, and slurry tests were conducted using methanol, acetone, and water. Kinetic profiles were modeled with the Kolmogorov–Johnson–Mehl–Avrami (KJMA) equation. Results: Polymorph A was thermodynamically stable across all analyses. Both amorphous TPZ and Polymorph B converted to A in a solvent-dependent manner. Methanol induced direct A formation, while acetone showed a B → A transition. Crystallization was guided by solution conformers and hydrogen bonding. Conclusions: TPZ polymorph selection is governed by solution-phase conformational preferences, tautomerism, and solvent-mediated hydrogen bonding. DFT-D and NMR analyses showed that protic solvents favor the direct crystallization of stable Polymorph A, while aprotic solvents promote the transient formation of metastable Polymorph B. Elevated temperatures and humidity accelerate polymorphic transitions. This crystal structure prediction (CSP)-independent strategy offers a practical framework for rational polymorph control and the mitigation of disappearing polymorph risks in tautomeric drugs. Full article

Houttuynia cordata is a culinary herb from Asia. Its edible rhizomes and leaves have a fishy aroma, the molecular background of which was unknown. A comparative aroma extract dilution analysis applied to fresh rhizomes and leaves resulted in 44 and 41 odorants, respectively, 38 of which were present with FD factors ≥1 in both samples. The odorant with the highest FD factors, whether in the rhizomes or leaves, was identified as metallic, soapy, fishy smelling 3-oxododecanal. Toward clarifying its tautomeric composition, quantum calculations suggested a predominance of the enol forms in the plant. However, the form perceived at the sniffing port during GC–O remained unclear. Full article

Surface-enhanced Raman scattering (SERS) spectroscopy is a straightforward analytical technique capable of providing detailed information about metabolites in biological samples. The objective of this study was to perform a SERS analysis of ergothioneine (EGT), an amino acid synthesized by microbes and fungi, across a range of pH values (acidic to alkaline) and concentrations (2 × 10⁻⁵ M to 2 × 10⁻⁷ M), to understand the dynamic interactions between EGT and silver (Ag) nanoparticles. Furthermore, SERS was applied in situ on mushroom fruiting bodies to detect the presence of EGT. The SERS spectra revealed that the interaction of EGT with Ag nanoparticles underwent significant alterations at varying pH levels, primarily due to isomerization. These changes were associated with modifications in the aromaticity and ionization of the imidazole ring, driven by both metal adsorption and alkaline conditions. Our results indicated the formation of distinct tautomeric forms of the imidazole group, namely the thione and thiol forms, in aqueous solution and on the Ag surface, respectively. Furthermore, the EGT spectra at different concentrations suggested that ionization occurred at lower concentrations. Notably, the SERS spectra of the mushroom fruiting bodies were dominated by prominent bands attributable to EGT, as corroborated by the comparison with the EGT fungal extract and EGT standard. These findings underscore the utility of SERS spectroscopy as a rapid and effective tool for obtaining comprehensive molecular fingerprints, even directly from complex biological matrices such as mushroom fruiting bodies. Full article

In the quest of the pivotal origin of the very strong gas-phase proton basicity for some iminopyrrole derivatives, proposed in the literature on the basis of quantum chemical calculations, the full tautomeric and acid/base equilibria were investigated in vacuo for 2-aminopyrrole exhibiting enamino–imino tautomerism. Thermochemistry of these processes investigated at the Density Functional Theory (DFT) level indicates a lower stability for the imino than for the enamino tautomers. However, the imino N atom in the imino forms displays an exceptionally high basicity, particularly in the minor and rare tautomers containing at least one tautomeric proton at the pyrrole C atom. This explains why derivatives of CH tautomers (being free of prototropy) display exceptionally high gas-phase proton basicity. As predicted by the Maksić group using quantum chemical methods, these derivatives can be considered as good organic imino N-superbase candidates. Unfortunately, some other structures of iminopyrrole derivatives (proposed by the same group) possess labile protons, and, thus, exhibit prototropy, resulting in the transformation into the more stable but less basic aminopyrrole derivatives under synthesis conditions or acid/base equilibria measurements. Full article

Previously, we have described a successful molecular switch (8-(benzo[d]thiazol-2-yl)quinolin-7-ol), working on the basis of long-range proton transfer. Bearing in mind that its switching efficiency in low-polarity aprotic solvents is not sufficient, in the current communication, we investigate in detail the effect of the substitution in the benzothiazole ring. By using the DFT approach, the ground-state stability of the tautomeric forms, involved in the switching process, is modeled with the aim of finding conditions where clean switching could be possible in variety of aprotic solvents. The results indicate that the substitution with electron-acceptor substituents could increase the switching efficiency, but the overall improvement depends on the positions and electronic effect of the particular substituent. Full article

Compounds with thiosemicarbazide and semicarbazide scaffolds are among the most promising structures in medicinal chemistry due to the possibility of forming multiple hydrogen bonds. Therefore, six new derivatives of 4-fluorophenoxyacetylthiosemicarbazide and 4-fluorophenoxyacetylthiosemicarbazide were designed to compare their physicochemical properties, biological activity, and in silico pharmacokinetic parameters. All compounds were characterized by ¹H, ¹³C NMR, ¹⁹F, IR spectra. For selected derivatives (AB2 and AB5), X-ray studies were performed to confirm their synthetic route and identify the tautomeric forms and intra- and intermolecular interactions occurring in the crystalline state. In the in silico pharmacokinetic study, a clear difference in lipophilicity was observed between thiosemicarbazide and semicarbazide derivatives. In vitro biological studies have shown the promising activity of thiosemicarbazides against prostate cancer cell line LNCaP, with a higher safety profile than semicarbazides. The most active compound AB2 showed IC₅₀ = 108.14 μM against LNCaP. Based on biological studies, topoisomerase IIα was proposed as a potential molecular target, which was confirmed by molecular docking studies. Full article

Tegoprazan is a potassium ion-competitive acid blocker (P-CAB) and a novel inhibitor of gastric acid secretion. The compound exists in two crystalline polymorphs, A and B, whose structures had not previously been reported. In this study, both polymorphs were analyzed by liquid- and solid-state NMR, revealing identical tautomeric states. Using this information, the crystal structures were determined from laboratory powder X-ray diffraction data by simulated annealing and Rietveld refinement. Both forms were found to crystallize in the monoclinic space group P2₁, with Z = 4 and two independent molecules in the asymmetric unit (Z′ = 2). To assess the stability and reliability of the refined structures, we attempted geometry optimization and vibrational analysis using DFT-D methods. However, due to the high conformational complexity of Z′ = 2 systems, these calculations failed to converge or produced imaginary frequencies. Instead, single-point energy calculations were performed on the refined models. The resulting relative energy differences, together with solubility data, van’t Hoff enthalpies, and DSC profiles, consistently indicated that Polymorph A is more stable than Polymorph B. These results highlight the challenges of structure validation via DFT-D for complex molecular crystals and demonstrate the value of integrating experimental and computational approaches for polymorph characterization. Full article

Ribavirin, 1-(β-D-Ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide, which is included in the list of drugs recommended in the guidelines for the diagnosis and treatment of SARS-CoV-2 infection, has been the subject of experimental and theoretical investigation. The most thermodynamically stable polymorphic form was studied using ¹H-¹⁴N NQR cross-relaxation, periodic DFT/QTAIM/RDS/3D Hirshfeld surfaces, and molecular docking. For the first time, a ¹H-¹⁴N cross-relaxation spectrum of ribavirin was recorded and interpreted. Twelve resonance frequencies were assigned to four inequivalent nitrogen positions in the molecule using combined experimental techniques and solid-state quantum chemical calculations. The influence of the structural alteration on the NQR parameters was modeled using GGA/RPBE. The differences in the binding pattern of ribavirin, acadesine, inosine, guanosine, and favipiravir-ribofuranosyl in the solid state and the protein-ligand complex were assessed to elucidate the differences in the binding mechanism at the molecular level due to aglycone modification. The replacement of the carbon adjacent to the ribose with nitrogen, in conjunction with the absence of oxygen at the 2-position of the ring, resulted in an increased flexibility of the RBV structure in comparison to the favipiravir-ribofuranosyl structure. The present study identified the intramolecular hydrogen bond NH···N in RBV as playing a crucial role in the formation of a quasi-five-membered ring. However, this bond was proven to be too weak to force positioning of the amide group in the ring plane. The ribofuranosyl in RBV inhibits tautomerism and freezes the conformation of the amide group. The results of the molecular dynamics simulations demonstrated that RBV and favipiravir-ribofuranosyl incorporated into the RNA primer exhibited comparable stability within the protein binding region. The titular anti-butterfly (inverted butterfly) effect is associated with the consequences of both the changes in aglycone moiety and the neighborhood alteration. Seven structure-binding strength indices and six novel quadrupolar indices defined in this study have been proven to facilitate the evaluation of the similarity of binding motifs in the solid state and protein-ligand complex. Full article

The so far unattended version of the Hirao reaction involving the coupling of the less reactive chloroarenes with >P(O)H reagents, such as diarylphosphine oxides, diethyl phosphite, and ethyl phenyl-H-phosphinate, was investigated in detail using Pd(OAc)₂ as the catalyst precursor, and applying some excess of the P-reagent to provide the ligand via its trivalent tautomeric (>P-OH) form. In the presence of triethylamine, no P–C coupling took place, meaning that there was a need for a stronger base, an alkali carbonate. The solvent had a significant effect on the efficiency of the Hirao reaction. The optimum conditions (10% of the Pd(OAc)₂, 1.3 equiv. of the P-reagent, 1.1 equiv. of the alkali carbonate, 135–150 °C) explored herein were applied in the synthesis of diaryl-phenylphosphine oxides, aryl-diphenylphosphine oxides, diethyl arylphosphonates, and ethyl diphenylphosphinate. Theoretical calculations performed at the M06-2X/6-31G(d,p)[PCM(MeCN)] level also justified coupling with the chloroarenes under appropriate conditions, and were in accord with the experimental results revealing the unsuitability of triethylamine as a base and the need for an alkali carbonate. The new protocol elaborated herein is more practical and “greener” than the version with bromoarenes, and embraces a wide substrate scope. Full article

A novel Schiff base, (E)-4-acetyl-N-(4-hydroxy-3-methoxybenzylidene)aniline (abbreviated as ANHMA), was synthesized and characterized using infrared and ¹H- and ¹³C-NMR spectroscopies. Optical properties in different solvents were evaluated using UV-vis absorption spectroscopy. The compound is shown to exhibit both positive and negative solvatochromism with reversal occurring for solvents with E_T(30)~45 (e.g., DMSO). The solvatochromic behavior of the compound was found to be strongly dependent on the hydrogen bond abilities and polarizability of the solvent, the observed reversal in solvatochromism being explained by the change in the dominant solvent effects in non-polar and polar–aprotic solvents (H-bond acceptor ability of the solvent and polarizability) compared to polar–protic solvents (H-bond donor ability), according to the developed Catalán multiparametric solvatochromic model. In all freshly prepared solutions studied, the (E)-enol-imine tautomer of the compound was found to strongly predominate over the keto-amine tautomeric forms, the latter increasing their populations over time in the presence of H-bond donor/acceptor species. Irradiation of ANHMA with UV light (λ ≥ 311 nm) was also investigated in several solvents and shown to follow a general pattern, with the conversion of the (E)-enol-imine tautomer into the keto-amine forms in a solvent-mediated enol-imine/keto-amine tautomerism, and (Z)→(E) C=C isomerization between the keto-imine forms. The experimental results received support from an extensive series of calculations on the structure and UV-vis spectra of the relevant tautomeric/isomeric forms of the compound performed at the DFT(B3LYP)/6-311++G(d,p) level of approximation (including time-dependent DFT calculations and solvent consideration). Full article

This study is focused on the effects of the sulphur atom in position 2 of the cytosine molecule, 2-thiocytosine (2TC), on the molecular structural parameters in the isolated state, as well as in the hydration, solid state arrangement, Watson–Crick pairs, and DNA–DNA microhelices, as compared to the canonical form. The main six tautomers were optimised at the MP2 and CCSD levels, and the sulphur atom does not show any effect on the stability trend of cytosine. The energy difference between T2b and T2a tautomers is twice as low in 2TC (1.15 kJ/mol) than in cytosine (2.69 kJ/mol). The IR and laser Raman spectra of 2TC were accurately assigned using DFT computations and solid-state simulations of the crystal unit cell through several tetramer forms. The results notably improve those previously published by other authors. The effect of explicit water molecules surrounding 2TC up to 30, corresponding to the first and second hydration shells, on geometries and tautomerism was analysed. The Watson–Crick base pairs’ stability (ΔE^CP = −97.458 kJ/mol) was found to be less than with cytosine (−105.930 kJ/mol). The calculated dipole moment was also lower (4.205 D) than with cytosine (5.793 D). The effect of 2TC on the 5′-dG-dC-dG-3′ and 5′-dA-dC-dA-3′ DNA–DNA optimised microhelices was evaluated through their calculated helical parameters, which indicates a clear deformation of the helix formation. The radius (R) with 2TC appears considerably shorter (6.200 Å) in the 5′-dA-dC-dA-3′ microhelix than that with cytosine (7.050 Å). Because of the special characteristics of the 2TC molecule, it can be used as an anticancer drug. Full article

Prototropic conversion (prototropy) for heterocyclic nucleobases was already signaled by Watson and Crick about seventy years ago as one of the reasons for nucleic acids mutations. This isomeric phenomenon has been investigated for neutral derivatives by means of both experimental and theoretical procedures, and their favored tautomers discussed in numerous articles published in the last fifty years. Protonation/deprotonation reactions in the gas phase have also been studied using both quantum-chemical calculations and experimental techniques. Some thermochemical parameters of these processes have been documented. However, prototropy has not always been taken into account in protonation/deprotonation reactions. Most frequently, tautomeric heterocycles have been treated as simple polyfunctional compounds without possible intramolecular protontransfers. Taking into account the lack of data for the complete tautomeric mixtures, quantum-chemical investigations have been undertaken by us about twenty-five years ago for prototropic heterosystems. In this work, the pyrimidine base uracil (U) was chosen. It possesses two identical exo groups (=O/OH) at the 2- and 4-positions, two labile (tautomeric) protons, and five conjugated sites (N1, N3, C5, O7, and O8). Different types of isomerism, prototropy and OH-rotation, were considered for the neutral, protonated, and deprotonated forms. Using quantum-chemical methods, thermochemical stabilities of all possible tautomers-rotamers were examined in vacuo and the potential isomers selected. The selected isomeric mixtures for the neutral and ionic forms were applied for the determination of the thermochemical parameters in the four-step acid/base equilibria: B²⁻ BH⁻ BH₂ BH₃⁺ BH₄²⁺, where BH₂ indicates U. For each step, the microscopic (kinetic) and macroscopic (thermodynamic) acid/base parameters were estimated, and sites of the proton gain and proton loss examined. The similarities and differences between the acid/base equilibria for uracil and other pyrimidine nucleobases were discussed. Full article

The current paradigm of low-T combustion and autoignition of hydrocarbons is based on the sequential two-step oxygenation of fuel radicals. The key chain-branching occurs when the second oxygenation adduct (OOQOOH) is isomerized releasing an OH radical and a key ketohydroperoxide (KHP) intermediate. The subsequent homolytic dissociation of relatively weak O–O bonds in KHP generates two more radicals in the oxidation chain leading to ignition. Based on the recently introduced intramolecular “catalytic hydrogen atom transfer” mechanism (J. Phys. Chem. 2024, 128, 2169), abbreviated here as I-CHAT, we have identified a novel unimolecular decomposition channel for KHPs to form their classical isomers—enol hydroperoxides (EHP). The uncertainty in the contribution of enols is typically due to the high computed barriers for conventional (“direct”) keto–enol tautomerization. Remarkably, the I-CHAT dramatically reduces such barriers. The novel mechanism can be regarded as an intramolecular version of the intermolecular relay transfer of H-atoms mediated by an external molecule following the general classification of such processes (Catal. Rev.-Sci. Eng. 2014, 56, 403). Here, we present a detailed mechanistic and kinetic analysis of the I-CHAT-facilitated pathways applied to n-hexane, n-heptane, and n-pentane models as prototype molecules for gasoline, diesel, and hybrid rocket fuels. We particularly examined the formation kinetics and subsequent dissociation of the γ-enol-hydroperoxide isomer of the most abundant pentane-derived isomer γ-C5-KHP observed experimentally. To gain molecular-level insight into the I-CHAT catalysis, we have also explored the role of the internal catalyst moieties using truncated models. All applied models demonstrated a significant reduction in the isomerization barriers, primarily due to the decreased ring strain in transition states. In addition, the longer-range and sequential H-migration processes were also identified and illustrated via a combined double keto–enol conversion of heptane-2,6-diketo-4-hydroperoxide as a potential chain-branching model. To assess the possible impact of the I-CHAT channels on global fuel combustion characteristics, we performed a detailed kinetic analysis of the isomerization and decomposition of γ-C5-KHP comparing I-CHAT with key alternative reactions—direct dissociation and Korcek channels. Calculated rate parameters were implemented into a modified version of the n-pentane kinetic model developed earlier using RMG automated model generation tools (ACS Omega, 2023, 8, 4908). Simulations of ignition delay times revealed the significant effect of the new pathways, suggesting an important role of the I-CHAT pathways in the low-T combustion of large alkanes. Full article

Push-pull imines with strong electron donor group(s) display exceptional basicity in the gas phase. Most of them do not exhibit prototropic tautomerism, and gas-phase acid-base equilibria have been already well described and reviewed. Some questions remain for tautomeric systems, particularly for their uncommon forms. As shown by quantum-chemical calculations, some often-neglected tautomers display higher basicity than the thermodynamically favored forms. However, their participation in tautomeric mixtures being in equilibrium is negligible, and their basicity can be impossible to measure in the gas phase by the equilibrium method. During this work, we examined the gas-phase proton basicity for some acyclic and cyclic push-pull organic bases containing the tautomeric amidine or guanidine group. By quantum-chemical calculations, we confirmed the existence of very low amounts of rare tautomeric forms, in particular, those bearing a methylidene (=CH₂) group. We also demonstrated that the alkyl derivatives of rare tautomers, being free of prototropy, can be good candidates as very strong push-pull C bases, i.e., bases protonated on the =CH₂ group. Full article