Positional Isomers Research Articles

Detection and Differentiation of Amines and N‐Heterocycles via Recognition Enabled Chromatographic 19F NMR

AbstractIn this study, we successfully employed a 19F‐labeled cyclopalladium probe to achieve simultaneous differentiation and detection of various amines and N‐heterocyclic compounds. This method features a broad detection window, facilitating the discrimination and multi‐component analysis of structural analogs and isomers through the generation of characteristic 19F NMR signals with distinct chemical shifts. The utility of this approach is demonstrated in monitoring chemical reactions and identifying components in food, beverages, and cosmetics.

Effect of perturbations on dantrolene - A DFT treatise

Dantrolene and an isomer of dantrolene which is obtained by a pair of centric perturbations (carbon to nitrogen replacement in N-N=CH moiety) are considered within the constraints of density functional theory at the level of B3LYP/6-31++G(d,p). Dantrolene is a skeletal muscle relaxant which interferes with the release of calcium ion from the sarcoplasmic reticulum. Both of the isomeric structures of present interest have exothermic heat of formation values and favorable Gibbs free energy of formation values. They are electronically stable as well. The perturbation results in a more exothermic and more favorable isomer than dantrolene. It is also electronically more stable than the parent structure. Various quantum chemical data have been collected and discussed including IR and UV-VIS spectra.

From mother's milk to structural insights: 1H–15N NMR analysis of Lewis X antigen-bearing oligosaccharides isolated from human milk

Human milk oligosaccharides (HMOs) are complex unconjugated glycans abundant in breast milk, with vital roles in infant nutrition and health. The structural elucidation of HMOs remains challenging due to their diverse compositions and isomeric complexities. This study presents a novel approach employing 1H–15N NMR correlations to pinpoint and characterize HMOs, LNH, LNnH, and their fucosylated derivatives including those of bearing the Lewis X motif. Isolated from human milk, these hexa-, hepta-, and octasaccharides were extensively analysed by NMR. This enabled their first complete 1H, 13C and 15N resonance assignments. Using 1H–15N HSQC experiments, the distinctive 1H–15N correlations of GlcNAc units within the HMOs provided structural fingerprints, allowing for unequivocal differentiation of isomeric structures and fucosylation patterns. Results demonstrate the potential of 1H–15N NMR spectroscopy in decoding complex HMO structures, offering new perspectives on their detailed structural characterization and contributing to a deeper understanding of their potential benefits.

The Addition of α-Hydroxy-benzylphosphonates to Dialkyl Acetyl­enedicarboxylates; Catalytic Hydrogenation of the Adducts

Abstractα-Hydroxy-benzylphosphonates obtained by the Pudovik reaction of substituted benzaldehydes and dialkyl phosphites were added to the triple bond of dialkyl acetylenedicarboxylates. Optimum conditions involved a 24 hours stirring in the presence of 10% diazabicycloundecene in dichloromethane to afford the adducts as a mixture of predominant E- and a minor Z-isomers in 75–90% yields after flash chromatography. The structures of the geometrical isomers were confirmed by NOE- and ROE-measurements. Catalytic hydrogenation of the olefinic moiety of the adducts led to the diastereoisomers of corresponding saturated derivatives.

Identification of a Chimera Mass Spectrum of Isomeric Lipid A Species Using Negative Ion Tandem Mass Spectrometry.

The toxic nature of bacterial endotoxins is affected by the structural details of lipid A, including the variety and position of acyl chains and phosphate group(s) on its diglucosamine backbone. Negative-ion mode tandem mass spectrometry is a primary method for the structure elucidation of lipid A, used independently or in combination with separation techniques. However, it is challenging to accurately characterize constitutional isomers of lipid A extracts by direct mass spectrometry, as the elemental composition and molecular mass of these molecules are identical. Thus, their simultaneous fragmentation leads to a composite, so-called chimera mass spectrum. The present study focuses on the phosphopositional isomers of the classical monophosphorylated, hexaacylated Escherichia coli-type lipid A. Collision-induced dissociation (CID) was performed in an HPLC-ESI-QTOF system. Energy-resolved mass spectrometry (ERMS) was applied to uncover the distinct fragmentation profiles of the phosphorylation isomers. A fragmentation strategy applying multi-levels of collision energy has been proposed and applied to reveal sample complexity, whether it contains only a 4'-phosphorylated species or a mixture of 1- and 4'-phosphorylated variants. This comparative fragmentation study of isomeric lipid A species demonstrates the high potential of ERMS-derived information for the successful discrimination of co-ionized phosphorylation isomers of hexaacylated lipid A.

Consequential Effect of Intake of Fatty Acid through Milk and Butterfat (Ghee)

Milk fat is observed to have high nutritional properties and other health benefits. The fat in milk is the most complicated natural fat since it comprises over 400 distinct fatty acids. The saturated fatty acids present in milk account for approximately 70% by weight (5). The most important fatty acid from a quantitative viewpoint is palmitic acid (16:0), which accounts for approximately 30% by weight of the total fatty acids. Myristic acid (14:0) and stearic acid (18:0) make up 11 and 12% by weight, respectively. Oleic acid is the major unsaturated fatty acid present in milk. The fatty acid composition of milk fat determines its nutritional value. The fatty acids found in milk vary in terms of their structure, cis or trans isomers, amount and location of double bonds, and chain length. The chemical makeup and content of the fatty acids present determine the physical and nutritional characteristics of the fat. The fatty acids in milk also have nutritional value and offer certain health advantages. Eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and other polyunsaturated fatty acids are considered to help prevent coronary artery disease (CAD) and other age-related neurodegenerative illnesses. Many of these therapeutic properties are unknown even today. The impact of fatty acids on human health is a topic that is always under dispute. Here we discuss how fatty acids act in terms of human health. Regulations have been implemented to ensure reduced risk due to the intake of fatty acids like trans fatty acids. Trans fats can increase the risk of CHD.

Serum N-Glycan Profiling of Patients with Narcolepsy Type 1 Using LC-MS/MS.

The neurological condition known as narcolepsy type 1 (NT1) is an uncommon condition marked by extreme daytime sleepiness, cataplexy, sleep paralysis, hallucinations, disrupted nocturnal sleep, and low or undetectable levels of orexin in the CSF fluid. NT1 has been hypothesized to be an immunological disorder; its treatment is currently only symptomatic, and misdiagnosis is not uncommon. This study compares the N-glycome of NT1 patients with healthy controls in search of potential glycan biomarkers using LC-MS/MS. A total of 121 candidate N-glycans were identified, 55 of which were isomeric N-glycan structures and 65 were not. Seventeen N-glycan biomarker candidates showed significant differences between the NT1 and control cohorts. All of the candidate glycan biomarkers were isomeric except HexNAc6Hex7Fuc0NeuAc1 (6701) and HexNAc6Hex7Fuc1NeuAc2 (6712). Therefore, with isomeric and nonisomeric structures, a total of 20 candidate N-glycan biomarkers are reported in this study, and interestingly, all are either sialylated or sialylated-fucosylated and upregulated in NT1 relative to the control. The distribution levels of all the identified N-glycans show that the sialylated glycan type is the most abundant in NT1 and is majorly disialylated, although the trisialylated subtype is three-fold higher in NT1 compared to the healthy control. The first isomers of HexNAc5Hex6Fuc0NeuAc3 (5603), HexNAc6Hex7Fuc0NeuAc2 (6702), and HexNAc6Hex7Fuc1NeuAc4 (6714) expressed a high level of fold changes (FC) of 1.62, 2.19, and 2.98, respectively. These results suggest a different N-glycome profile of NT1 and a relationship between sialylated glycan isomers in NT1 disease development or progression. The revelation of N-glycan expression alterations in this study may improve NT1 diagnostic methods, understanding of NT1 pathology, and the development of new targeted therapeutics.

Closing Kok’s cycle of nature’s water oxidation catalysis

The Mn4CaO5(6) cluster in photosystem II catalyzes water splitting through the Si state cycle (i = 0–4). Molecular O2 is formed and the natural catalyst is reset during the final S3 → (S4) → S0 transition. Only recently experimental breakthroughs have emerged for this transition but without explicit information on the S0-state reconstitution, thus the progression after O2 release remains elusive. In this report, our molecular dynamics simulations combined with density functional calculations suggest a likely missing link for closing the cycle, i.e., restoring the first catalytic state. Specifically, the formation of closed-cubane intermediates with all hexa-coordinate Mn is observed, which would undergo proton release, water dissociation, and ligand transfer to produce the open-cubane structure of the S0 state. Thereby, we theoretically identify the previously unknown structural isomerism in the S0 state that acts as the origin of the proposed structural flexibility prevailing in the cycle, which may be functionally important for nature’s water oxidation catalysis.

Effect of Solvent Properties on the Critical Solution Temperature of Thermoresponsive Polymers.

The ability of thermoresponsive polymers to respond to temperature with a reversible conformational change makes them promising 'smart' materials for solutions in medical and biotechnological applications. In this work, two such polymers and structural isomers were studied: poly(N-isopropyl acrylamide) (PNiPAm) and poly(2-isopropyl-2-oxazoline) (PiPOx). We compare the critical solution temperatures (CST) of these polymers in D2O and H2O in the presence of Hofmeister series salts, as results obtained under these different solvent conditions are often compared. D2O has a higher dipole moment and electronegativity than H2O, which could significantly alter the CST transition. We used two complementary methods to measure the CST, dynamic light scattering (DLS) and differential scanning calorimetry (DSC) and found that the CST decreased significantly in D2O compared to H2O. In the presence of highly concentrated kosmotropes, the CST of both polymers decreased in both solvents. The influence of the kosmotropic anions was smaller than the water isotope effect at low ionic strengths but considerably higher at physiological ionic strengths. However, the Hofmeister anion effect was quantitatively different in H2O than in D2O, with the largest relative differences observed for Cl-, where the CSTs in D2O decreased more than in H2O measured by DLS but less by DSC. PiPOx was more sensitive than PNiPAm to the presence of chaotropes. It exhibited much higher transition enthalpies and multistep transitions, especially in aqueous solutions. Our results highlight that measurements of thermoresponsive polymer properties in D2O cannot be compared directly or quantitatively to application conditions or even measurements performed in H2O.

Poly(alkylene 2,4-furanoate)s: The potential of structural isomerism for outstanding sustainable food packaging and unexpected evidence of self-healing microstructure

2,5-furandicarboxylic acid is an extremely appealing renewable chemical building block because of its potential to replace the petrochemical and industrially widespread terephthalic acid via the synthesis of poly(alkylene 2,5-furanoate)s (2,5-PAF). The recent interest in its structural isomer, 2,4-furandicarboxylic acid (2,4-FDCA), opened the study of poly(alkylene 2,4-furanoate)s (2,4-PAF). In this work, 2,4-FDCA was polymerized with linear glycols of increasing chain length, via a solvent-free polycondensation reaction, obtaining high molecular weight 2,4-PAF. Namely, poly(trimethylene 2,4-furanoate) (2,4-PTF), poly(pentamethylene 2,4-furanoate) (2,4-PPeF) and poly(hexamethylene 2,4-furanoate) (2,4-PHF). These polyesters were compression molded into films and subjected to NMR, GPC, WAXS, PLOM, TGA and DSC analyses. The functional properties for food packaging applications were evaluated by mechanical and gas permeability tests. 2,4-PAF had tunable mechanical properties, depending on the glycol used, and in some cases, the mechanical behavior of a thermoplastic elastomer and shape recovery after break. In particular, 2,4-PPeF had outstanding gas barrier properties, while DSC analyses on 2,4-PHF showed an endothermic phenomenon attributed to the isotropization of a partially-ordered phase: it was possible to demonstrate that this phase was disrupted during tensile tests and slowly recovered over time, at room temperature. Overall, the results offer new insights into the structure-property relationships of poly(alkylene 2,4-furanoate)s and display their great potential for the production of biobased, monomaterial, easily recyclable and sustainable food packaging.

Filling the gaps in peptide maps with a platform assay for top-down characterization of purified protein samples.

Liquid chromatography-mass spectrometry (LC-MS) intact mass analysis and LC-MS/MS peptide mapping are decisional assays for developing biological drugs and other commercial protein products. Certain PTM types, such as truncation and oxidation, increase the difficulty of precise proteoform characterization owing to inherent limitations in peptide and intact protein analyses. Top-down MS (TDMS) can resolve this ambiguity via fragmentation of specific proteoforms. We leveraged the strengths of flow-programmed (fp) denaturing online buffer exchange (dOBE) chromatography, including robust automation, relatively high ESI sensitivity, and long MS/MS window time, to support a TDMS platform for industrial protein characterization. We tested data-dependent (DDA) and targeted strategies using 14 different MS/MS scan types featuring combinations of collisional- and electron-based fragmentation as well as proton transfer charge reduction. This large, focused dataset was processed using a new software platform, named TDAcquireX, that improves proteoform characterization through TDMS data aggregation. A DDA-based workflow provided objective identification of αLac truncation proteoforms with a two-termini clipping search. A targeted TDMS workflow facilitated the characterization of αLac oxidation positional isomers. This strategy relied on using sliding window-based fragment ion deconvolution to generate composite proteoform spectral match (cPrSM) results amenable to fragment noise filtering, which is a fundamental enhancement relevant to TDMS applications generally.

Synthesis and Properties of a Strained Triple Nanohoop.

A strained triple nanohoop with a shared central benzene unit is synthesized using a threefold intramolecular ring-closing approach. Among the five possible constitutional isomers, the isomer with the highest D3h symmetry is isolated, the structure of which contains three nanohoop blades and a central hexaphenylbenzene unit. The structure is elucidated using NMR spectroscopy and mass spectrometry. The optical and electrochemical properties are investigated, revealing a moderate fluorescence quantum yield of 40 %. A water-soluble nanomaterial is prepared using a nanoparticle encapsulation method, and a fluorescence quantum yield of 10 % is retained, which demonstrates the potential of the nanomaterial in biological systems.

Master equation modeling of water dissociation in small ionic water clusters: Ag+(H2O) n , n = 4-6.

We model temperature-dependent blackbody infrared radiative dissociation (BIRD) rate coefficients of Ag+(H2O) n , n = 4-6, a system with loosely bound water molecules. We employ a master equation modeling (MEM) approach with consideration of absorption and emission of blackbody radiation, comparing single and multiple-well descriptions. The unimolecular dissociation rate coefficients are obtained using the Rice-Ramsperger-Kassel-Marcus (RRKM) theory, employing two approaches to model the sum of states in the transition state, the rigid activated complex (RAC) and the phase space limit (PSL) approach. A genetic algorithm is used to find structures of low-lying isomers for the kinetic modeling. We show that the multiple-well MEM approach with PSL RRKM in the All Wells and Transition States Are Relevant (AWATAR) variant provides a reliable description of Ag+(H2O) n BIRD, in agreement with previously published experimental data. Higher-lying isomers contribute significantly to the overall dissociation rate coefficient, underlying the importance of the multiple-well ansatz in which all isomers are treated on the same footing.

Primordial aqueous alteration recorded in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu

We report primordial aqueous alteration signatures in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu by the Hayabusa2 spacecraft of JAXA. Newly identified low-molecular-weight hydroxy acids (HO-R-COOH) and dicarboxylic acids (HOOC-R-COOH), such as glycolic acid, lactic acid, glyceric acid, oxalic acid, and succinic acid, are predominant in samples from the two touchdown locations at Ryugu. The quantitative and qualitative profiles for the hydrophilic molecules between the two sampling locations shows similar trends within the order of ppb (parts per billion) to ppm (parts per million). A wide variety of structural isomers, including α- and β-hydroxy acids, are observed among the hydrophilic molecules. We also identify pyruvic acid and dihydroxy and tricarboxylic acids, which are biochemically important intermediates relevant to molecular evolution, such as the primordial TCA (tricarboxylic acid) cycle. Here, we find evidence that the asteroid Ryugu samples underwent substantial aqueous alteration, as revealed by the presence of malonic acid during keto–enol tautomerism in the dicarboxylic acid profile. The comprehensive data suggest the presence of a series for water-soluble organic molecules in the regolith of Ryugu and evidence of signatures in coevolutionary aqueous alteration between water and organics in this carbonaceous asteroid.

Identification of synthetic cathinone positional isomers using electron activated dissociation mass spectrometry

BackgroundSynthetic cathinones (SCs) are a large category of new psychoactive substances (NPS), which pose a serious threat to public health due to limited information about their toxicology and pharmacology. Many SCs are closely related in their chemical structures, with some substances being positional isomers. In this study, we propose a new workflow for the identification of SC isomers using liquid chromatography-high-resolution tandem mass spectrometry (LC-HRMS2) combined with electron activated dissociation (EAD) and chemometrics. Differentiation between isomeric SCs is essential for both legislative and public safety reasons, since minor differences in their molecular structures may change their legal status and pharmacological profiles. ResultsThe workflow was optimized using ring-substituted isomers of methylmethcathinones, methylethcathinones, and chloromethcathinones. The kinetic energy in the EAD cell was investigated at three levels (i.e., 15, 18, and 20 eV) for each group. Two data analysis methods (i.e., t-distributed stochastic neighbor embedding [t-SNE] and a Random Forest [RF] algorithm) were applied using the obtained EAD mass spectral data. The three sets of ring-substituted SCs were clearly distinguished using t-SNE and an RF algorithm. Moreover, the RF approach resulted in a 97 % classification accuracy for isomer identification using various combinations of compounds, isomers, and electron kinetic energies. This workflow was subsequentially applied to the analysis of 26 blind street samples, resulting in a 92 % classification accuracy for isomer identification. However, the accuracy varied based on the kinetic electron energy. A subset of the original data set, focusing on 15-eV data only, was used, resulting in a classification accuracy of 100 %. SignificanceThis study presents the first LC-HRMS2 workflow based on EAD and chemometrics, which resulted in a classification accuracy of 100 % of authentic street samples. The developed LC-HRMS2 workflow demonstrates that EAD product ions and their characteristic ion ratios can be successfully used to identify ring-substituted positional isomers of SCs.

A dual-labeling molecule for efficient drug discovery of mitochondrial-lysosomal interactions

The close association between organelle interactions, such as mitochondrial–lysosomal interactions, and various diseases, including tumors, remains a challenge for drug discovering and identification. Conventional evaluation methods are often complex and multistep labeling procedures often generate false positives, such as cell damage. To overcome these limitations, we employed a single dual-color reporting molecule called Coupa, which labels mitochondria and lysosomes as blue and red, respectively. This facilitates the evaluation and discovering of drugs targeting mitochondria–lysosome contact (MLC). Using Coupa, we validated the effectiveness of various known antitumor drugs in intervening MLC by assessing their effect on key aspects, such as status, localization, and quantity. This provides evidence for the accuracy and applicability of our dual-color reporting molecule. Notably, we observed that several structural isomers of drugs, including Urolithin (A/B/C), exhibited distinct effects on MLC. In addition, Verteporfin and TEAD were found to induce anti-tumor effects by controlling MLC at the organelle level, suggesting a potential new mechanism of action. Collectively, Coupa offers a novel scientific tool for discovering drugs that target mitochondrial–lysosomal interactions. It not only distinguished the differential effects of structurally similar drugs on the same target, but also reveals new mechanisms underlying the reported antitumor properties of existing drugs. Ultimately, our findings contribute to the advancement of drug discovery and provide valuable insights into the complex interactions between organelles in a disease context.

Dithiophosphonate-Protected Eight-Electron Superatomic Ag21 Nanocluster: Synthesis, Isomerism, Luminescence, and Catalytic Activity.

The structure-property relationship considering isomerism-tuned photoluminescence and efficient catalytic activity of silver nanoclusters (NCs) is exclusive. Asymmetrical dithiophosphonate NH4[S2P(OR)(p-C6H4OCH3)] ligated first atomically precise silver NCs [Ag21{S2P(OR)(p-C6H4OCH3)}12]PF6 {where, R = nPr (1), Et (2)} were established by single-crystal X-ray diffraction and characterized by electrospray ionization mass spectrometry, NMR (31P, 1H, 2H), X-ray photoelectron spectroscopy, UV-visible, energy-dispersive X-ray spectroscopy, Fourier transforms infrared, thermogravimetric analysis, etc. NCs 1 and 2 consist of eight silver atoms in a cubic framework and enclose an Ag@Ag12-centered icosahedron to constitute an Ag21 core of Th symmetry, which is concentrically inscribed within the S24 snub-cube, P12 cuboctahedron, and the O12 truncated tetrahedron formed by 12 dithiophosphonate ligands. These NCs facilitate to be an eight-electron superatom (1S21P6), in which eight capping Ag atoms exhibit structural isomerism with documented isoelectronic [Ag21{S2P(OiPr)2}12]PF6, 3. In contrast to 3, the stapling of dithiophosphonates in 1 and 2 triggered bluish emission within the 400 to 500 nm region at room temperature. The density functional theory study rationalized isomerization and optical properties of 1, 2, and 3. Both (1, and 2) clusters catalyzed a decarboxylative acylarylation reaction for rapid oxindole synthesis in 99% yield under ambient conditions and proposed a multistep reaction pathway. Ultimately, this study links nanostructures to their physical and catalytic properties.

Separating and identifying multiple structural isomers of 3-hydroxy-3-(3′-hydroxyphenyl)propanoic acid (3,3′-HPHPA)

3-hydroxy-3-(3′-hydroxyphenyl)propanoic acid (CID: 102959) (3,3’-HPHPA) is one of several phenolic molecules that are generated by a process involving gut microbiota and have been implicated in autism and schizophrenia. The structural isomers of 3,3′-HPHPA have been challenging to separate chromatographically. Accordingly, their distribution across brain and other compartments in humans and experimental animals remains poorly characterized. We describe a modified liquid chromatography mass spectroscopy method for the detection and separation of seven commercially available structural isomers of 3,3′-HPHPA. We used the method to screen different compartments in the mouse and demonstrate its utility in identifying multiple structural isomers and conjugates of 3,3′-HPHPA in biological matrices. Characterizing the diversity and complexity of this family of structural isomers will advance studies of their bioactivity and clinical relevance.

Illuminating the dark space of neutral glycosphingolipidome by selective enrichment and profiling at multi-structural levels

Glycosphingolipids (GSLs) are essential components of cell membranes, particularly enriched in the nervous system. Altered molecular distributions of GSLs are increasingly associated with human diseases, emphasizing the significance of lipidomic profiling. Traditional GSL analysis methods are hampered by matrix effect from phospholipids and the difficulty in distinguishing structural isomers. Herein, we introduce a highly sensitive workflow that harnesses magnetic TiO2 nanoparticle-based selective enrichment, charge-tagging Paternò–Büchi reaction, and liquid chromatography-tandem mass spectrometry. This approach enables mapping over 300 distinct GSLs in brain tissues by defining sugar types, long chain bases, N-acyl chains, and the locations of desaturation and hydroxylation. Relative quantitation of GSLs across multiple structural levels provides evidence of dysregulated gene and protein expressions of FA2H and CerS2 in human glioma tissue. Based on the structural features of GSLs, our method accurately differentiates human glioma with/without isocitrate dehydrogenase genetic mutation, and normal brain tissue.

Canniprene B, a new prenylated dihydrostilbene with cytotoxic activities from the leaves of Cannabis sativa

A new, canniprene B (4), along with five known (1–3 and 5–6) dihydrostilbenes were isolated from the leaves of Cannabis sativa collected at CSIR – IIIM, Jammu, India. Structures of all isolated compounds were elucidated by spectroscopic data analysis, including 1D and 2D NMR, and HR-ESI-MS. Canniprene B is a new prenylated dihydrostilbenes, a positional isomer of the known compound canniprene (5). The cytotoxic activities of these compounds (1–6) were evaluated using the SRB assay against a panel of five human cancer cell lines. Notably, canniprene B (4) exhibited varying levels of cytotoxicity with IC50 values ranging from 2.5 to 33.52 μM, demonstrating the most potent activity against pancreatic cancer cells.