NMR Studies Research Articles

Hydrogen Bonding in Amorphous Indomethacin.

Amorphous Indomethacin has enhanced bioavailability over its crystalline forms, yet amorphous forms can still possess a wide variety of structures. Here, Empirical Potential Structure Refinement (EPSR) has been used to provide accurate molecular models on the structure of five different amorphous Indomethacin samples, that are consistent with their high-energy X-ray diffraction patterns. It is found that the majority of molecules in amorphous Indomethacin are non-bonded or bonded to one neighboring molecule via a single hydrogen bond, in contrast to the doubly bonded dimers found in the crystalline state. The EPSR models further indicate a substantial variation in hydrogen bonding between different amorphous forms, leading to a diversity of chain structures not found in any known crystal structures. The majority of hydrogen bonds are associated with the carboxylic acid group, although a significant number of amide hydrogen bonding interactions are also found in the models. Evidence of some dipole-dipole interactions are also observed in the more structurally ordered models. The results are consistent with a distribution of Z-isomer intramolecular type conformations in the more disordered structures, that distort when stronger intermolecular hydrogen bonding occurs. The findings are supported by 1H and 2H NMR studies of the hydrogen bond dynamics in amorphous Indomethacin.

Experimental and theoretical study of the photochemical properties and acidochromism of nonconventional 2,4,6-triarylpyridine-based materials

2,4,6-Triarylpyridines (TAPs) represent a versatile class of N-heterocycles with broad applications in many fields. This study presents an investigation on photochemical properties and acidochromism behavior of novel 2,6-bis(4-(dodecyloxy)phenyl)-4-(4-substituted-phenyl)pyridine-based derivatives (1a-1g). Photochemical study in dichloromethane (DCM) and acetone (ACT) solutions showed a small solvent effect for the TAP derivatives, except for the carbazole derivative 1a, which was characterized as the most emissive material in all conditions, but especially in DCM solution for blue emission (λEM = 406 nm, ϕf = 0.36). The presence of electron-donating groups at the 4-phenyl moiety contributes to more intense and redshifted emissions in both DCM and ACT solutions, as well as in the solid state. In aqueous ACT, while TAPs bearing EDGs such as 1a presented more intense emissions depending on the water fraction, an opposite effect was verified for fluorinated derivative 1f. The acidochromism of selected TAPs 1a and 1f (fluorinated derivative) in aqueous acetone was characterized by the decreasing of the emission intensity at 436 nm and 388 nm, respectively, in the presence of aqueous HCl for both TAPs, however, the protonated 1f showed strong emission in higher wavelength (λEM = 476 nm) in acidic medium. A 1H NMR study allowed a better understanding of the structural features associated to the acidochromism. The photochemical and acidochromism results obtained for the TAP derivatives are strongly supported by computational results, and particularly noteworthy is the favoring of the resonance effect as consequence of the decreasing in the torsion angle between the 4-alkoxyaryl substituents and the pyridine core after protonation of 1f. The emissive properties and acidochromism capacity of 1a and 1f allowed the potential application of TAP-adsorbed paper strips as disposable sensors for qualitative detection of gaseous HCl.

Inhibition of protein tyrosine phosphatase 1B by serratane triterpenes from Huperzia serrata and their molecular docking study

During the search for protein tyrosine phosphatase 1B (PTP1B) inhibitory compounds from the natural resources, two new serratane triterpenes, 3-O-dihydro-p-coumaroyltohogenol (1) and 21-O-acetyltohogenol (2), along with four known serratane triterpenes (3–6), were isolated from the whole plant of Huperzia serrata. The chemical structures of compounds 1 and 2 were determined by NMR study, HRMS analysis, and chemical modification. All isolates were evaluated for their PTP1B inhibitory activities. Among the isolates, compounds 1, 3, 5 and 6 exhibit moderate inhibitory activities against PTP1B. Kinetic studies demonstrated that they are competitive inhibitors. Molecular docking studies support these experimental results by showing that compounds 1, 3, 5 and 6 interact with the active site of PTP1B, clarifying the structure–activity relationship. This study suggests that serratane triterpenes from H. serrata have potential as starting skeletons for anti-diabetes or anti-obesity agents.

Rational Design of Highly Selective Sialyllactose-Imprinted Nanogels.

We describe a facile method to prepare water-compatible molecularly imprinted polymer nanogels (MIP NGs) as synthetic antibodies against target glycans. Three different phenylboronic acid (PBA) derivatives were explored as monomers for the synthesis of MIP NGs targeting either α2,6- or α2,3-sialyllactose, taken as oversimplified models of cancer-related sT and sTn antigens. Starting from commercially available 3-acrylamidophenylboronic acid, also its 2-substituted isomer and the 5-acrylamido-2-hydroxymethyl cyclic PBA monoester derivative were initially evaluated by NMR studies. Then, a small library of MIP NGs imprinted with the α2,6-linked template was synthesized and tested by mobility shift Affinity Capillary Electrophoresis (msACE), to rapidly assess an affinity ranking. Finally, the best monomer 2-acrylamido PBA was selected for the synthesis of polymers targeting both sialyllactoses. The resulting MIP NGs display an affinity constant≈106 M-1 and selectivity towards imprinted glycans. This general procedure could be applied to any non-modified carbohydrate template possessing a reducing end.

Biophysical studies of human serum albumin with cocaine and cocaethylene: Understanding the drug-protein interaction in simulated physiological conditions

In this study, HSA was used as a transport protein model to simulate the transport dynamics and availability of cocaine (COC) and its pharmacologically active metabolite, cocaethylene (CE). In the interaction studies between the alkaloids and HSA, the binding constant (Kb) values were higher for CE (2.92 to 8.33 × 104 M−1) than COC (1.15 to 3.77 × 104 M−1) at different temperatures. Thermodynamic parameter calculations indicate that COC preferentially interacts through van der Waals forces and hydrogen bonds, while CE interacts hydrophobically. Competition studies using the ANS probe confirmed the more hydrophobic characteristics of CE. Synchronized fluorescence indicated that both compounds preferentially interact in the microregion of the Trp214 residue. Based on 3D fluorescence, UV–vis, and circular dichroic results, changes in the secondary structure of the protein were confirmed. Studies to assess the HSA binding site were carried out using warfarin (site I), diazepam (site II), and digitoxin (subdomain IIIB) as markers, and it was verified that both compounds interact preferentially at the site I. Finally, based on the 1H NMR and theoretical studies, it was possible to propose the alkaloid epitope in the interaction with HSA. In conclusion, when compared to COC, CE presented greater HSA protein affinity, justifying its longer plasma lifetime and increasing the drug’s effects on the body.

1H-NMR-based metabolomics reveals metabolic alterations in early development of a mouse model of Angelman syndrome

BackgroundAngelman syndrome (AS) is a rare neurodevelopmental genetic disorder caused by the loss of function of the ubiquitin ligase E3A (UBE3A) gene, affecting approximately 1:15,000 live births. We have recently shown that mitochondrial function in AS is altered during mid to late embryonic brain development leading to increased oxidative stress and enhanced apoptosis of neural precursor cells. However, the overall alterations of metabolic processes are still unknown. Hence, as a follow-up, we aim to investigate the metabolic profiles of wild-type (WT) and AS littermates and to identify which metabolic processes are aberrant in the brain of AS model mice during embryonic development.MethodsWe collected brain tissue samples from mice embryos at E16.5 and performed metabolomic analyses using proton nuclear magnetic resonance (1H-NMR) spectroscopy. Multivariate and Univariate analyses were performed to determine the significantly altered metabolites in AS mice. Pathways associated with the altered metabolites were identified using metabolite set enrichment analysis.ResultsOur analysis showed that overall, the metabolomic fingerprint of AS embryonic brains differed from those of their WT littermates. Moreover, we revealed a significant elevation of distinct metabolites, such as acetate, lactate, and succinate in the AS samples compared to the WT samples. The elevated metabolites were significantly associated with the pyruvate metabolism and glycolytic pathways.LimitationsOnly 14 metabolites were successfully identified and investigated in the present study. The effect of unidentified metabolites and their unresolved peaks was not determined. Additionally, we conducted the metabolomic study on whole brain tissue samples. Employing high-resolution NMR studies on different brain regions could further expand our knowledge regarding metabolic alterations in the AS brain. Furthermore, increasing the sample size could reveal the involvement of more significantly altered metabolites in the pathophysiology of the AS brain.ConclusionsUbe3a loss of function alters bioenergy-related metabolism in the AS brain during embryonic development. Furthermore, these neurochemical changes could be linked to the mitochondrial reactive oxygen species and oxidative stress that occurs during the AS embryonic development.

DMNP as an Effective Cage for Ln3+: A Spectroscopic and Thermodynamic Study.

Dimethoxynitrophenyl-EDTA (DMNP) is a popular calcium cage that is frequently used to investigate the role of Ca2+ in signaling processes in vivo. Lanthanides have been used in Ca2+ biomimetics due to similarities in coordination properties of Ln3+ and Ca2+ that may enable fluorescence and NMR studies of functional and structural properties of Ca2+ binding proteins. In this study, we show that Tb3+, Eu3+, and Nd3+ bind strongly to DMNP in a 1:1 ratio. Isothermal titration calorimetric measurements of Ca2+ displacement by Ln3+ in DMNP provide the equilibrium binding constants for Ln3+DMNP complexation with association constants, K11 = (1.2 ± 0.7) × 1012 M-1 for Eu3+, (2.5 ± 1.7) × 1012 M-1 for Nd3+, and (2.8 ± 0.8) × 1012 M-1 for Tb3+. The kinetics and thermodynamics of Ca2+, Mg2+, and Tb3+ release from DMNP were characterized using photothermal beam deflection (PBD). Ligand release from the DMNP cage was rapid and occurred within 10 μs upon cage photofragmentation and was associated with similar reaction volume and enthalpy changes that can be attributed to the photoreleased ion solvation. In the case of Ca2+DMNP photodissociation at subsaturating Ca2+ concentrations, we observed a slower phase with a lifetime of 300 μs that we attribute to Ca2+ rebinding to unphotolyzed DMNP. These results demonstrate that DMNP can serve as an effective photolabile cage for oxophilic Ln3+ that has similar coordination properties to Ca2+ and Mg2+.

Corrigendum: This article corrects the following: Pt‐WOx/C Catalysts for α, β‐Unsaturated Aldehydes Hydrogenation: An NMR Study of the Effect of the Reactant Adsorption on Activity and Selectivity

Corrigendum: This article corrects the following: Pt‐WO_x/C Catalysts for α, β‐Unsaturated Aldehydes Hydrogenation: An NMR Study of the Effect of the Reactant Adsorption on Activity and Selectivity

Probing Short-Range Interactions in Isostructural Hydrate and Perhydrate of Dabrafenib by Magic-Angle Spinning Solid-State NMR.

Dabrafenib (DBF), an anticancer drug, exhibits isostructural properties in its hydrate (DBF⊃H2O) and perhydrate (DBF⊃H2O2) forms, as revealed by single-crystal X-ray diffraction. Despite the H2O and H2O2 solvent molecules occupying identical locations, the two polymorphs have different thermal behaviors. In general, determination of stoichiometry of H2O in the perhydrate crystals is difficult due to the presence of both H2O and H2O2 in the same crystal voids. This study utilizes magic-angle spinning (MAS) solid-state NMR (SSNMR) combined with gauge-included projector augmented wave calculations to characterize the influence of solvent molecules on the local environment in pseudopolymorphs. SSNMR experiments were employed to assign 1H, 13C, and 15N peaks and identify spectral differences in the isostructural pseudopolymorphs. Proton spectroscopy at fast MAS was used to identify and quantify H2O2/H2O in DBF⊃H2O2 (mixed hydrate/perhydrate). 1H-1H dipolar-coupling-based experiments were recruited to confirm the 3D molecular packing of solvent molecules in DBF⊃H2O and DBF⊃H2O2. Homonuclear (1H-1H) and heteronuclear (1H-14N) distance measurements, in conjunction with diffraction structures and optimized hydrogen atom positions by density functional theory, helped decipher local interactions of H2O2 with DBF and their geometry in DBF⊃H2O2. This integrated X-ray structure, quantum chemical calculations, and NMR study of pseudopolymorphs offer a practical approach to scrutinizing crystallized solvent interactions in the crystal lattice even without high-resolution crystal structures or artificial sample enrichment.

Probing rotaxane dynamics with 19F NMR/MRI: Unveiling the roles of mechanical bond and steric hindrance

BackgroundDeciphering the molecular dynamics (MD) of rotaxanes is crucial for designing and refining their applications in molecular devices. This study employed fluorine-19 nuclear magnetic resonance (19F NMR) and magnetic resonance imaging (MRI) to unveil the interplay between mechanical bonds and steric hindrance in a series of fluorinated rotaxanes. Results1H/19F NMR revealed stable “Z”-shaped wheel conformations minimizing steric clashes and favoring π-π interactions with the axle. Utilizing fluorines and axle protons as reporters, 1H/19F relaxation rates and solid-state 19F NMR studies demonstrated that mechanical bond primarily governs wheel motion, while steric hindrance dictates axle movement. Intriguingly, mechanical bond mainly affects local axle groups, leaving distant ones minimally impacted. MD simulations corroborated these findings. Temperature-dependent 19F NMR indicated that energy input enhances rotational motion and wheel conformational transitions. Furthermore, the drastic increase in 19F relaxation rates upon mechanical bond formation and steric hindrance enables sensitive and selective 19F MRI visualization of MD changes. SignificanceThis study, by elucidating the roles of internal and external factors on rotaxane molecular dynamics using 19F NMR/MRI, offers valuable insights that can advance the field of rotaxane-based molecular devices.

Tuning the textural properties of biomass-derived nanocrystallized BEA for acetyl functionalization of anisole

The synthesis of a highly active zeolite beta catalyst for acetyl functionalization of anisole by utilizing the silica precursor obtained from rice husk is a promising approach for the mitigation of agricultural waste. The influence of combustion temperature (CT) (300, 500, 700, and 900 °C) on the characteristics of rice husk ash was investigated. The C52H obtained at a medium CT (500 °C) has a high surface area compared to the C72H indicates that, merging of smaller crystals of amorphous silica to form crystalline silica with larger crystallites by applying more thermal energy when CT ≥ 700 °C. The PS-5 catalyst derived from C52H possess high surface area (332 m2/g) and a smaller crystallite size (14.8 nm) compared to the PS-7 obtained from C72H, which shown the lower surface area (131.5 m2/g) with a larger crystallite size (25.6 nm). Solid-state NMR and NH3-TPD analysis reveals that PS-5 catalyst possessing higher acidity compare to both PS and PS-7. The activity studies confirms that the PS-5 catalyst exhibited superior catalytic activity (>98%) compared to PS (conventional) and PS-7 catalysts, making it a potential candidate for continuous production of aromatic ketones. acylation reactions.

Chiral Diselenophosphoric Acids for Ion Pair Catalysis: A Novel Approach to Enhance Both Proton Donating and Proton Accepting Properties.

The activation of poorly reactive substrates via strong chiral acids is a central topic in asymmetric ion pair catalysis these days. Despite highly successful scaffolds such as N-triflylphosphoramides, these catalysts either lack C2-symmetry or provide multiple H-bond acceptor sites, leading to lower ee values for certain reactions. We present BINOL-based diselenophosphoric acids (DSA) as an extremely promising alternative. Using an intertwined approach of synthesis and NMR studies, we developed a synthetic approach to DSA with up to 98 % NMR yield. The obtained acids provide both very high proton donor and proton acceptor properties, a bifunctionality, which is key to catalytic applications. Indeed, first reactivity test proved the much higher acidity of DSA and its ability to initiate Mukaiyama-Mannich reaction and protodesilylation of silyl ethers. Together with their C2-symmetry, the single donor and single acceptor situation, the decreased tendency of self-association, and the straightforward synthesis with potential 3,3'-substitution, the DSA provide all features ideal for the further development of ion pair catalysis.

Synthesis, characterization, DFT and docking studies of tributyltin(IV) complex of 2-{4-hydroxy-3-[(2-carboxyphenylimino)methyl]phenylazo} benzoic acid

A tributyltin(IV) complex was prepared by reacting bis-tributyltin(IV) oxide with 2-{4-hydroxy-3-[(2-carboxyphenylimino)methyl]phenylazo}benzoic acid in a 1:1 metal-ligand ratio. The complex was characterized by elemental analysis, UV-Vis, IR,1H and 119Sn NMR spectroscopy and mass spectrometry techniques. The 119Sn NMR study of the complex indicated the presence of two tin centers in a similar chemical environment and the complex exhibited a five-coordinate trigonal bipyramidal geometry in the solution phase. The molecular ion peak in the EI-MS spectrum of the complex revealed its molar mass. The optimized geometry of the complex was predicted by a DFT calculation. The in vitro antifungal activity of the complex was studied against four fungal species with respect to the standard drug Amphotericin-B. A molecular docking study was also carried out to understand the mode of interaction of the complex with the active side of the enzyme present in fungal species.

Synthesis, Structure, and Resolution of Functionalized Oxacalix[4]arenes with Planar Chirality via Dynamic SNAr Reaction

A pair of racemic oxacalix[4]arenes featuring planar chirality and a mesomer with a symmetric plane were conveniently synthesized under mild conditions via a one‐pot dynamic SNAr reaction and separated in 20% and 49% yields, respectively. X‐ray single crystal analyses confirmed their structures unambiguously. The racemic mixture could further be resolved using HPLC on a chiral column. Time‐dependent products distribution and interconversion between products with CsF as a catalyst were revealed by 1H NMR studies, convincing the dynamic nature of SNAr reaction.

Computational NMR Study of Benzothienoquinoline Heterohelicenes.

Early NMR studies of several heterohelicenes containing an annular nitrogen atom and a thiophene ring in their structure suggested the possibility of the lengthening of the carbon-carbon bonds in the interior of the helical turn of the molecule based on the progressive upfield shift of 13C resonances toward the center of the helical turn. We now report a comprehensive analysis of the optimized geometry and a comparison of the calculated vs. observed 1H and 13C NMR chemical shifts of nineteen representative benzothienoquinoline heterohelicenes. As was initially hypothesized on the basis of the progressive upfield shift of carbon resonances toward the center of the interior helical turn, the present computational study has demonstrated that carbon-carbon bonds indeed have more sp3 character and are longer than normal sp2 bonds to accommodate the helical twist of the molecule, as expected.

Chalcogen Bonding in Selective Recognition and Liquid-Liquid Extraction of Perrhenate.

Efficient recognition and extraction of hazardous anionic pollutants from water medium is of great significance for environmental concerns, representing a challenging area of research in supramolecular chemistry. In this study, we present, for the first time, a comprehensive demonstration of the ability of chalcogen bonding (ChB) to recognize and remove the ReO4 - from 100 % water medium. The anion recognition ability is well elucidated through solution phase NMR and ITC studies, which clearly reveal the selective binding of ReO4 - over other oxo-anions. Moreover, the selenoimidazolium scaffold effectively engages in Se•••O ChB interaction with ReO4 - as confirmed by X-ray crystal structure and XPS analysis. More importantly, the binding of ReO4 - with different prolongations of the σ-holes, along with Se•••Se chalcogen bonding interactions, lead to the formation of a 1D supramolecular assembly. Eventually, ChB receptor Se4Me-Br exhibits ~62 % ReO4 - extraction efficiency through precipitation as the extraction method. Furthermore, in efforts to enhance efficiency, a hydrophobic ChB receptor Se4Do-PF6 has been prepared, achieving an efficiency of up to ~93 % at a very low concentration (~5 ppm) by liquid-liquid extraction.

Solid‐Phase‐Supported Chemoenzymatic Synthesis and Analysis of Chondroitin Sulfate Proteoglycan Glycopeptides

AbstractProteoglycans (PGs), consisting of glycosaminoglycans (GAGs) linked with the core protein through a tetrasaccharide linkage region, play roles in many important biological events. The chemical synthesis of PG glycopeptides is extremely challenging. In this work, the enzymes required for synthesis of chondroitin sulfate (CS) PG (CSPG) have been expressed and the suitable sequence of enzymatic reactions has been established. To expedite CSPG synthesis, the peptide acceptor was immobilized on solid phase and the glycan units were directly installed enzymatically onto the peptide. Subsequent enzymatic chain elongation and sulfation led to the successful synthesis of CSPG glycopeptides. The CS dodecasaccharide glycopeptide was the longest homogeneous CS glycopeptide synthesized to date. The enzymatic synthesis was much more efficient than the chemical synthesis of the corresponding CS glycopeptides, which could reduce the total number of synthetic steps by 80 %. The structures of the CS glycopeptides were confirmed by mass spectrometry analysis and NMR studies. In addition, the interactions between the CS glycopeptides and cathepsin G were studied. The sulfation of glycan chain was found to be important for binding with cathepsin G. This efficient chemoenzymatic strategy opens new avenues to investigate the structures and functions of PGs.

Solid-Phase-Supported Chemoenzymatic Synthesis and Analysis of Chondroitin Sulfate Proteoglycan Glycopeptides.

Proteoglycans (PGs), consisting of glycosaminoglycans (GAGs) linked with the core protein through a tetrasaccharide linkage region, play roles in many important biological events. The chemical synthesis of PG glycopeptides is extremely challenging. In this work, the enzymes required for synthesis of chondroitin sulfate (CS) PG (CSPG) have been expressed and the suitable sequence of enzymatic reactions has been established. To expedite CSPG synthesis, the peptide acceptor was immobilized on solid phase and the glycan units were directly installed enzymatically onto the peptide. Subsequent enzymatic chain elongation and sulfation led to the successful synthesis of CSPG glycopeptides. The CS dodecasaccharide glycopeptide was the longest homogeneous CS glycopeptide synthesized to date. The enzymatic synthesis was much more efficient than the chemical synthesis of the corresponding CS glycopeptides, which could reduce the total number of synthetic steps by 80 %. The structures of the CS glycopeptides were confirmed by mass spectrometry analysis and NMR studies. In addition, the interactions between the CS glycopeptides and cathepsin G were studied. The sulfation of glycan chain was found to be important for binding with cathepsin G. This efficient chemoenzymatic strategy opens new avenues to investigate the structures and functions of PGs.

Organocatalytic asymmetric synthesis of Si-stereogenic silacycles

A strong and confined Brønsted acid catalyzed enantioselective cyclization of bis(methallyl)silanes provides enantioenriched Si-stereogenic silacycles. High enantioselectivities of up to 96.5:3.5 er were obtained for a range of bis(methallyl)silanes. NMR and ESI-MS studies reveal that the formation of a covalent adduct irreversibly inhibits turnover. Remarkably, we found that acetic acid as an additive promotes the collapse of this adduct, enabling full turnover. Experimental investigation and density functional theory (DFT) calculations were conducted to elucidate the origin of this phenomenon and the observed enantioselectivity.

Structural basis of water-mediated cis Watson-Crick/Hoogsteen base-pair formation in non-CpG methylation.

Non-CpG methylation is associated with several cellular processes, especially neuronal development and cancer, while its effect on DNA structure remains unclear. We have determined the crystal structures of DNA duplexes containing -CGCCG- regions as CCG repeat motifs that comprise a non-CpG site with or without cytosine methylation. Crystal structure analyses have revealed that the mC:G base-pair can simultaneously form two alternative conformations arising from non-CpG methylation, including a unique water-mediated cis Watson-Crick/Hoogsteen, (w)cWH, and Watson-Crick (WC) geometries, with partial occupancies of 0.1 and 0.9, respectively. NMR studies showed that an alternative conformation of methylated mC:G base-pair at non-CpG step exhibits characteristics of cWH with a syn-guanosine conformation in solution. DNA duplexes complexed with the DNA binding drug echinomycin result in increased occupancy of the (w)cWH geometry in the methylated base-pair (from 0.1 to 0.3). Our structural results demonstrated that cytosine methylation at a non-CpG step leads to an anti→syntransition of its complementary guanosine residue toward the (w)cWH geometry as a partial population of WC, in both drug-bound and naked mC:G base pairs. This particular geometry is specific to non-CpG methylated dinucleotide sites in B-form DNA. Overall, the current study provides new insights into DNA conformation during epigenetic regulation.