Search Results (95)

A series of water-soluble molecules based on 8-isopropyl-2-methyl-5-nitroquinoline and 1,10-phenanthroline core were designed by introducing a π-conjugated bridge, vinyl unit –CH=CH–. We present the selective conversion of methyl groups located on the C2 and C9 positions in the constitution of selected quinoline or 1,10-phenanthroline derivatives, respectively, into vinyl (or styryl) products by applying Perkin condensation. The two groups of ligands differ in the presence of one or two arms. The structure of the molecule ((1E,1′E)-(1,10-phenanthroline-2,9-diyl)bis(ethene-2,1-diyl))bis(benzene-4,1,3-triyl) tetraacetate was determined by single-crystal X-ray diffraction measurements. The X-ray, NMR, and DFT computational studies indicate the influence of rotation (rotamers) on the physical properties of studied styryl molecules. The results show that the styryl molecules with the vinyl unit –CH=CH– exhibit significant static and dynamic hyperpolarizabilities. Quantum chemical calculations using density functional theory and B3LYP/6-311++G(d,p) with Grimme’s dispersion correction approach predict the existence and relative stability of different spatial cis(Z)- and trans(E)-conformers of styryl derivatives of quinoline and 1,10-phenanthroline, which exhibit different electronic distribution and conjugation within the molecular skeleton, dipole moments, and steric interactions, leading to variations in their photophysical behavior and various applications. Our studies indicate that the rotation and isomerization of aryl groups can significantly influence the electronic and optical properties of π-conjugated systems, such as vinyl units (–CH=CH–). The rotation of aryl groups around the single bond that connects them to the vinyl unit can lead to changes in the effective π-conjugation between the aryl group and the rest of the π-conjugated system. The rotation and isomerization of aryl groups in π-conjugated systems significantly impact their electronic and optical properties. These changes can modify the efficiency of π-conjugation, affecting charge transfer processes, absorption properties, light emission, and electrical conductivity. In designing optoelectronic materials, such as organic dyes, organic semiconductors, or electrochromic materials, controlling the rotation and isomerization of aryl groups can be crucial for optimizing their functionality. Full article

The structural analysis of glycans remains a major challenge due to their high isomeric complexity and conformational flexibility arising from diverse glycosidic linkages and dynamic three-dimensional structures. Ion mobility–mass spectrometry (IM–MS) has been attracting attention as a way to develop the structural analysis of glycans. In this study, the effects of ionization conditions—including different types of adduct ions, ionization temperatures, and solvent environments—on the ion mobility behavior of glycans were systematically investigated. IM–MS measurements of ethylamine-tagged glycans showed broad arrival time distributions of monoprotonated ions indicating the presence of multiple conformers of glycans. Increased ionization temperatures and the use of methanol as a solvent further broadened the distribution, suggesting the enhanced conformational dynamics of the glycan ions. In contrast, sodium adduct ions yielded narrower distributions, implying that the interactions between sodium ions and glycans constrained structural flexibility. These results demonstrate that ionization parameters have a significant impact on glycan conformational behavior and mobility in the gas phase. This study provides insights into the analytical conditions for IM–MS measurements of glycans and highlights the utility of this method as a powerful tool for elucidating glycan structure and dynamics. Full article

A comprehensive theoretical investigation of the C₃H₂O potential energy surface (PES) was conducted, revealing 30 equilibrium structures (EQs), 128 transition state structures (TSs), and 35 direct dissociation channels (DCs), establishing a global reaction network comprising 101 isomerization pathways and dissociation channels. Particular focus was placed on the five most stable isomers, H₂CCCO (EQ3), OC(H)CCH (EQ7), H-c-CC(O)C-H (EQ0), HCC(H)CO (EQ1), and HO-c-CCC-H (EQ12), and their reactions with water molecules. Multicomponent artificial force-induced reaction (MC-AFIR) calculations were employed to study bimolecular collisions between H₂O and these stable isomers. The product distributions revealed isomer-specific reactivity patterns: EQ3 and EQ7 predominantly formed neutral species at high collision energies, EQ0 produced both ionic and neutral species, while EQ1 and EQ12 exhibited more accessible reaction pathways at lower collision energies with a propensity for spontaneous isomerization. Born–Oppenheimer Molecular Dynamics (BOMD) simulations complemented these findings, suggesting several viable products emerge from reactions with water molecules, including HCCC(OH)₂H (EQ7 + H₂O), OCCHCH₂OH (EQ1 + H₂O), and HO-c-CC(H)C(OH)-H (EQ12 + H₂O). This investigation elucidates the intrinsic relationships between isomers and their potential products, formed through biomolecular collisions with water molecules, establishing a fundamental framework for future conformational and reactivity studies of the C₃H₂O family. Full article

Prolyl cis/trans isomerization is a rate-limiting step in protein folding, often coupling directly to the acquisition of native structure. Here, we investigated the interplay between folding and prolyl isomerization in the N2 domain of the gene-3-protein from filamentous phage fd, which adopts a native-state cis/trans equilibrium at Pro161. Using mutational and Φ-value analysis, we identified a discrete folding nucleus encompassing the β-strands surrounding Pro161. These native-like interactions form early in the folding pathway and provide the energy to shift the cis/trans equilibrium toward the cis form. Variations distant from the Pro161-loop have minimal impact on the cis/trans ratio, underscoring the spatial specificity and localized control of the isomerization process. Using NMR spectroscopy, we determined the structures for both native N2 forms. The cis- and trans-Pro161 conformations are overall identical and exhibit only slight differences around the Pro161-loop. The cis-conformation adopts a more compact structure with improved backbone hydrogen bonding, explaining the approximately 10 kJ·mol⁻¹ stability increase of the cis state. Our findings highlight that prolyl isomerization in the N2 domain is governed by a localized folding nucleus rather than global stability changes. This localized energetic coupling ensures that proline isomerization is not simply a passive, slow step but an integral component of the folding landscape, optimizing both the formation of native structure and the establishment of the cis-conformation. Full article

Biliverdin reductase B (BLVRB) is a redox regulator that catalyzes nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reductions of multiple substrates, including flavins and biliverdin-β. BLVRB has emerging roles in redox regulation and post-translational modifications, highlighting its importance in various physiological contexts. In this study, we explore the structural and functional differences between human BLVRB and its hyrax homologue, focusing on evolutionary adaptations at the active site and allosteric regions. Using NMR spectroscopy, we compared coenzyme binding, catalytic turnover, and dynamic behavior between the two homologues. Despite lacking the arginine “clamp” present in human BLVRB, hyrax BLVRB still undergoes conformational changes in response to the oxidative state of the coenzyme. Mutations at the allosteric site (position 164) show that threonine at this position enhances coenzyme discrimination and allosteric coupling in human BLVRB, while hyrax BLVRB does not display the same allosteric effects. Relaxation experiments revealed distinct dynamic behaviors in hyrax BLVRB, with increased flexibility in its holo form due to the absence of the clamp. Our findings suggest that the evolutionary loss of the active site clamp and modifications at position 164 in hyrax BLVRB alter the enzyme’s conformational dynamics and coenzyme interactions. Identified similarities and differences underscore how key regions modulate catalytic efficiency and suggest that coenzyme isomerization may represent the rate-limiting step in both homologues. Full article

Ethyl maltol was investigated using matrix isolation infrared spectroscopy and DFT calculations. In an argon matrix (14.5 K), the compound was found to exist in a single conformer (form I), characterized by an intramolecular hydrogen bond with an estimated energy of ~17 kJ mol⁻¹. The IR spectrum of this conformer was assigned, and the molecule’s potential energy landscape was explored to understand the relative stability and isomerization dynamics of the conformers. Upon annealing the matrix to 41.5 K, ethyl maltol was found to predominantly aggregate into a centrosymmetric dimer (2× conformer I) bearing two intermolecular hydrogen bonds with an estimated energy of ca. 28 kJ mol⁻¹ (per bond). The UV-induced (λ > 235 nm) photochemistry of the matrix-isolated ethyl maltol was also investigated. After 1 min of irradiation, band markers of two rearrangement photoproducts formed through the photoinduced detachment-attachment (PIDA) mechanism, in which the ethyl maltol radical acts as an intermediate, were observed: 1-ethyl-3-hydroxy-6-oxibicyclo [3.1.0] hex-3-en-2-one and 2-ethyl-2H-pyran-3,4-dione. The first undergoes subsequent reactions, rearranging to 4-hydroxy-4-propanoylcyclobut-2-en-1-one and photofragmenting to cyclopropenone and 2-hydroxybut-1-en-1-one. Other final products were also observed, specifically acetylene and CO (the expected fragmentation products of cyclopropenone), and CO₂. Overall, the study demonstrated ethyl maltol’s high reactivity under UV irradiation, with significant photochemical conversion occurring within minutes. The rapid photochemical conversion, with complete consumption of the compound in 20 min, should be taken into account in designing practical applications of ethyl maltol. Full article

This study investigates the chemical structure of profoxydim, focusing on its E–isomer, the main commercial form. The research aimed to determine the predominant tautomeric forms under various environmental conditions. Using proton and carbon–13 NMR spectroscopy alongside theoretical modeling, we examined tautomers and their conformers in different solvents (MeOD, DMSO, CDCl₃, benzene) to mimic gas and aqueous phases. The findings reveal that the enolic form dominates in the gas phase, while the ketonic form prevails in aqueous environments, providing key insights into the herbicide’s environmental behavior. We also observed an isomeric transition from E to Z under acidic conditions, which could affect profoxydim’s reactivity in natural environments. The theoretical calculations indicated that in acidic conditions, the E and Z forms are nearly degenerate, with the E form remaining dominant in neutral environments. Additionally, QSAR models assessed the toxicity of various tautomers, revealing significant differences that could impact bioactivity and environmental fate. This research offers crucial insights into the structural dynamics of profoxydim, contributing to cyclohexanedione chemistry and the development of more effective herbicides. Full article

It is generally accepted that adjacent guanine residues in DNA are the primary target for platinum antitumor drugs and that differences in the conformations of the Pt-DNA adducts can play a role in their antitumor activity. In this study, we investigated the effect of the carrier ligand cis-1,3-diaminocyclohexane (cis-1,3-DACH) upon formation, stability, and stereochemistry of the (cis-1,3-DACH)PtG₂ and (cis-1,3-DACH)Pt(d(GpG)) adducts (G = 9-EthlyGuanine, guanosine, 5′- and 3′-guanosine monophosphate; d(GpG) = deoxyguanosil(3′-5′)deoxyguanosine). A peculiar feature of the cis-1,3-DACH carrier ligand is the steric bulk of the diamine, which is asymmetric with respect to the Pt-coordination plane. The (cis-1,3-DACH)Pt(5′GMP)₂ and (cis-1,3-DACH)Pt(3′GMP)₂ adducts show preference for the ΛHT and ∆HT conformations, respectively (HT stands for Head-to-Tail). Moreover, the increased intensity of the circular dichroism signals in the cis-1,3-DACH derivatives with respect to the analogous cis-(NH₃)₂ species could be a consequence of the greater bite angle of the cis-1,3-DACH carrier ligand with respect to cis-(NH₃)₂. Finally, the (cis-1,3-DACH)Pt(d(GpG)) adduct is present in two isomeric forms, each one giving a pair of H8 resonances linked by a NOE cross peak. The two isomers were formed in comparable amounts and had a dominance of the HH conformer but with some contribution of the ΔHT conformer which is related to the HH conformer by having the 3′-G base flipped with respect to the 5′-G residue. Full article

Two structural isomeric porphyrin-based triads (Zn(II)porphyrin−Sn(IV)porphyrin−Zn(II)porphyrin) denoted as T1 and T2 were prepared from the reaction of meso-[5-(4-hydroxyphenyl)-10,15,20-tris(3,5-di-tert-butylphenyl)porphyrinato]zinc(II) (ZnL) with trans-dihydroxo-[5,10-bis(3-pyridyl)-15,20-bis(phenyl)porphyrinato]tin(IV) (SnP¹) and trans-dihydroxo-[5,15-bis(3-pyridyl)-10,20-bis(phenyl)porphyrinato]tin(IV) (SnP²), respectively. All the compounds were characterized using UV–vis spectroscopy, emission spectroscopy, ESI−MS, ¹H NMR spectroscopy, and FE-SEM. Most importantly, the two structurally isomeric porphyrin-based triads supramolecularly self-assembled into completely different nanostructures. T1 exhibits a nanosphere morphology, whereas T2 exhibits a nanofiber morphology. The amplified geometric feature in the structural isomeric porphyrin-based triads dictates the physical and chemical properties of the two triads. Both compounds showed the morphology-dependent visible light catalytic photodegradation of rhodamine B dye (74–97% within 90 min) and tetracycline antibiotic (44–71% within 45 min) in water. In both cases, the photodegradation efficiency of T2 was higher than that of T1. The present investigation can significantly contribute to the remediation of wastewater by tuning the conformational changes in porphyrin-based photocatalysts. Full article

Cytotoxins (CTs) are three-finger membrane-active toxins present mainly in cobra venom. Our analysis of the available CT amino acid sequences, literature data on their membrane activity, and conformational equilibria in aqueous solution and detergent micelles allowed us to identify specific amino acid residues which interfere with CT incorporation into membranes. They include Pro9, Ser28, and Asn/Asp45 within the N-terminal, central, and C-terminal loops, respectively. There is a hierarchy in the effect of these residues on membrane activity: Pro9 > Ser28 > Asn/Asp45. Taking into account all the possible combinations of special residues, we propose to divide CTs into eight groups. Group 1 includes toxins containing all of the above residues. Their representatives demonstrated the lowest membrane activity. Group 8 combines CTs that lack these residues. For the toxins from this group, the greatest membrane activity was observed. We predict that when solely membrane activity determines the cytotoxic effects, the activity of CTs from a group with a higher number should exceed that of CTs from a group with a lower number. This classification is supported by the available data on the cytotoxicity and membranotropic properties of CTs. We hypothesize that the special amino acid residues within the loops of the CT molecule may indicate their involvement in the interaction with non-lipid targets. Full article

Thiazolin-4-ones and their derivatives represent important heterocyclic scaffolds with various applications in medicinal chemistry. For that reason, the synthesis of two 5-substituted thiazolidin-4-one derivatives was performed. Their structure assignment was conducted by NMR experiments (2D-COSY, 2D-NOESY, 2D-HSQC and 2D-HMBC) and conformational analysis was conducted through Density Functional Theory calculations and 2D-NOESY. Conformational analysis showed that these two molecules adopt exo conformation. Their global minimum structures have two double bonds (C=N, C=C) in Z conformation and the third double (C=N) in E. Our DFT results are in agreement with the 2D-NMR measurements. Furthermore, the reaction isomerization paths were studied via DFT to check the stability of the conformers. Finally, some potential targets were found through the SwissADME platform and docking experiments were performed. Both compounds bind strongly to five macromolecules (triazoloquinazolines, mglur3, Jak3, Danio rerio HDAC6 CD2, acetylcholinesterase) and via SwissADME it was found that these two molecules obey Lipinski’s Rule of Five. Full article

The geometrical r_e parameters of trans-azobenzene (E-AB) free molecule were refined by gas electron diffraction (GED) method using available experimental data obtained previously by S. Konaka and coworkers. Structural analysis was carried out by various techniques. First of all, these included the widely used molecular orbital constrained gas electron diffraction method and regularization method. The results of the refinements using different models were also compared—a semirigid model, three variants of one-dimensional dynamic models, and a two-dimensional pseudoconformer model. Several descriptions have been used due to the fact that E-AB has a shallow potential energy surface along the rotation coordinates of phenyl groups. Despite this, it turned out that the semirigid model is suitable for use for E-AB and allows good agreement with experimental data to be achieved. According to the results of GED structural analysis, coupled with the results of DLPNO-CCSD(T0) calculations, E-AB has a planar structure. Based only on GED data, it is impossible to unambiguously determine the rotational angle of the phenyl group due to the facts that (i) with rotation over a wide range of angles, the bonded distances in the molecule change insignificantly and (ii) potential function in a structural analysis within a dynamic model is not determined with the necessary accuracy. This work also examines the sensitivity of the GED method to structural changes caused by trans-cis isomerization. The paper also analyzes the applicability of different variants of density functional theory (DFT) calculations in GED structural analysis using E-AB as an example. There are not enough similar methodological works in the literature. This experimental and methodological information is especially important and relevant for planning and implementing GED experiments and corresponding processing of the results for azobenzene derivatives, in which the conformer and isomeric diversity are even more complicated due to the presence of different substituents. Full article

Xylose isomerase (XI, also known as glucose isomerase) is an oxidoreductase that interconverts aldoses and ketoses. XI catalyzes the reversible isomerization of D-glucose and D-xylose into D-fructose and D-xylulose, respectively. The molecular function of XI is widely applied in producing high-fructose corn syrup (HFCS) in the food industry and bioethanol from hemicellulose in the biofuel industry. The structural information of XI from diverse strains is important for understanding molecular properties that can provide insights into protein engineering to improve enzyme efficiency. To extend the knowledge of the structural information on XI, the crystal structure of XI from Streptomyces avermitilis (SavXI) was determined at a 2.81 Å resolution. SavXI containing TIM barrel and extended α-helix domains formed the tetrameric assembly. The two metal-binding sites and their coordinating residues showed diverse conformations, providing the structural flexibility of the active site of SavXI. The structural comparison of SavXI and XI homologs exhibited unique metal-binding sites and conformations of the C-terminal α-helix domain. These structural results extend our knowledge of the molecular flexibility and mechanism of the XI family. Full article

Many folding enzymes use separate domains for the binding of substrate proteins and for the catalysis of slow folding reactions such as prolyl isomerization. FKBP12 is a small prolyl isomerase without a chaperone domain. Its folding activity is low, but it could be increased by inserting the chaperone domain from the homolog SlyD of E. coli near the prolyl isomerase active site. We inserted two other chaperone domains into human FKBP12: the chaperone domain of SlpA from E. coli, and the chaperone domain of SlyD from Thermococcus sp. Both stabilized FKBP12 and greatly increased its folding activity. The insertion of these chaperone domains had no influence on the FKBP12 and the chaperone domain structure, as revealed by two crystal structures of the chimeric proteins. The relative domain orientations differ in the two crystal structures, presumably representing snapshots of a more open and a more closed conformation. Together with crystal structures from SlyD-like proteins, they suggest a path for how substrate proteins might be transferred from the chaperone domain to the prolyl isomerase domain. Full article

In order to look for the origins of tautomeric preferences in neutral creatinine in vacuo, we examined prototropic conversions for model azoles, namely mono-hydroxy and mono-amino imidazoles, and also for their selected 1-methyl derivatives. All possible isomeric forms of creatinine and model compounds, resulting from intramolecular proton transfer (prototropy), conformational isomerism about –OH, and configurational isomerism about =NH, were studied in the gas phase (model of non-polar environment) by means of quantum-chemical methods. Because the bond-length alternation is a consequence of the resonance phenomenon, it was measured for all DFT-optimized structures by means of the harmonic oscillator model of electron delocalization (HOMED) index. Important HOMED analogies were discussed for investigated azoles and compared with those for previously studied cyclic azines, including pyrimidine nucleic acid bases. The internal effects were taken into account, and the stabilities of the investigated tautomers-rotamers were analyzed. Significant conclusions on the favored factors that can dictate the tautomeric preferences in creatinine were derived. Full article