Oxonium Ion Research Articles

A Study on Polymerization of Oxocane High Explosives

Oxocane high explosives substituted to explosive group such as azide (-CH2N3), nitrate (-CH2ONO2), and hydrazine (-CH2N2H3) are investigated theoretically the acid catalyzed reaction using the semiempirical MINDO/3, MNDO and AM1 methods to use as the guidelines of high explosives. The nucleophilicity and basicity of oxocane high explosives can be explained by the value of negative charge on oxygen atom of oxocane and the reactivity in propagation step can be represented by the value of positive charge on carbon atom and low electrophile LUMO energy. It was known that carbenium ion was favorable due to the stable energy (11.745~25.461 Kcal/mol) between oxonium ion and carbenium ion in the process of cyclic oxonium ion of oxocane high explosives being converted to open carbenium ion in oxocane high explosives. The value of concentration of cyclic oxonium ion and open carbenium ion in equilibrium status was found to be a major determinant of mechanism, it was expected to react faster in the prepolymer propagation step in SN1 mechanism than in that of SN2.

Assignment of saccharide identities through analysis of oxonium ion fragmentation profiles in LC-MS/MS of glycopeptides.

Protein glycosylation plays critical roles in the regulation of diverse biological processes, and determination of glycan structure-function relationships is important to better understand these events. However, characterization of glycan and glycopeptide structural isomers remains challenging and often relies on biosynthetic pathways being conserved. In glycoproteomic analysis with liquid chromatography-tandem mass spectrometry (LC-MS/MS) using collision-induced dissociation (CID), saccharide oxonium ions containing N-acetylhexosamine (HexNAc) residues are prominent. Through analysis of beam-type CID spectra and ion trap CID spectra of synthetic and natively derived N- and O-glycopeptides, we found that the fragmentation patterns of oxonium ions characteristically differ between glycopeptides terminally substituted with GalNAcα1-O-, GlcNAcβ1-O-, Galβ3GalNAcα1-O-, Galβ4GlcNAcβ-O-, and Galβ3GlcNAcβ-O- structures. The difference in the oxonium ion fragmentation profiles of such glycopeptides may thus be used to distinguish among these glycan structures and could be of importance in LC-MS/MS-based glycoproteomic studies.

In-depth analysis of site-specific N-glycosylation in vitronectin from human plasma by tandem mass spectrometry with immunoprecipitation.

The characterization of site-specific microheterogeneity in glycoprotein is very important for understanding cell biology and disease processes. Vitronectin is well known to be a multifunctional glycoprotein in the blood and the extracellular matrix, which is related to hepatocellular carcinoma (HCC). Here, we systematically analyzed the site-specific N-glycopeptides of vitronectin in human plasma by tandem mass spectrometry combined with immunoprecipitation and hydrophilic interaction liquid chromatography (HILIC) enrichment. Vitronectin was purified with immunoprecipitation by monoclonal antibody from plasma and digested to tryptic N-glycopeptides.Then, enrichment with HILIC materials was used and followed by analysis with nano-LC/MS/MS. The sequences of N-glycopeptides were identified from the mass spectra by high-energy C-trap dissociation (HCD) and collision-induced dissociation (CID). In HCD mode, oxonium ions were used for recognizing glycopeptides and y ions for sequencing the peptide backbone. In CID mode, Y ions were used for characterizing their glycoforms. As a result, a total of 17 site-specific N-glycopeptides were completely identified in all of the three N-glycosylation sites of vitronectin in human plasma, including 12 N-glycopeptides first reported. Finally, we specifically found that three hybrid and four complex glycopeptides of triantennary forms with outer fucosylation increased in HCC human plasma.

Rational Design of Oxirane Monomers for Efficient Crossover Reactions in Concurrent Cationic Vinyl-Addition and Ring-Opening Copolymerization with Vinyl Ethers

Rational structural design of oxirane monomers is demonstrated here to be highly conducive to crossover reactions in the concurrent cationic vinyl-addition and ring-opening copolymerization of alkyl vinyl ethers and oxiranes. The key to the efficient crossover reactions was the smooth transformation of the once-formed oxirane-derived oxonium ion into the ring-opened carbocation, which then reacted with a vinyl monomer. For example, oxiranes that form resonance-stabilized, allyl-type carbocations (i.e., isoprene monoxide and butadiene monoxide) were polymerized through efficient crossover reactions in copolymerization with isopropyl vinyl ether, yielding copolymers composed of relatively short monomer sequences. In particular, the copolymerization of isoprene monoxide and isopropyl vinyl ether generated random or alternating-rich copolymers. The reaction using an oxirane that forms tertiary carbocations (isobutylene oxide) also proceeded via crossover reactions; however, the crossover frequency was lower, which resulted in a multiblock-like copolymer. In contrast to the three oxiranes that yielded copolymers, oxiranes that possibly result in secondary carbocations from their ring-opening (3,3-dimethyl-1,2-butylene oxide and 1,2-butylene oxide) hardly induced crossover reactions. In addition to the ease of carbocation generation via ring-opening, the nucleophilicity of the monomer and the reactivity of the oxirane-derived carbocations were shown to substantially affect the copolymerization behavior. These factors are discussed on the basis of the monomer reactivity ratios that were determined for the copolymerization systems using vinyl ethers with different reactivities, i.e., isopropyl vinyl ether or ethyl vinyl ether, toward oxiranes.

Synthesis of 3′,4′-difluoro-3′-deoxyribonucleosides and its evaluation of the biological activities: Discovery of a novel type of anti-HCV agent 3′,4′-difluorocordycepin

Upon reacting 3′,4′-unsaturated cytosine (8 and 9) and adenine nucleosides (13 and 14) with XeF2/BF3·OEt2, the respective novel 3′,4′-difluoro-3′-deoxyribofuranosyl nucleosides (10–12 and 15–18) could be obtained. Formation of anti-adducts (11, 16 and 18) revealed that the fluorination involved oxonium ions as incipient intermediates. TBDMS-protected 3′,4′-unsaturated adenosine provided the β-face adducts as sole stereoisomers whereas α-face-selectivity was observed with the TBDPS-protected adenosine 14. The evaluation of the novel 3′-deoxy-3′,4′-difluororibofuranosylcytosine-(19–21) and adenine nucleosides (22–25) against antitumor and antiviral activities revealed that 3′,4′-difluorocordycepin (24) was found to possess anti-HCV activity. The SI of 24 was comparable to that of the anti-HCV drug ribavirin. However, sofosbuvir, FDA-approved novel anti-HCV drug, showed better SI value. Our finding revealed that the introduction of the fluoro-substituent into the 4′-position of cordycepin derivatives decreased the cytotoxicity to the host cell with retention of the antiviral activity.

Synthesis of polyketide stereoarrays enabled by a traceless oxonia-Cope rearrangement.

Polyketide antibiotics bearing skipped polyols represent a synthetic challenge. A SiCl4-promoted oxonia-Cope rearrangement of syn,syn-2-vinyl-1,3-diols was developed to forge an array of 1,5-pentenediols, thus providing versatile motifs for the preparation of 1,2,3,5-stereoarrays in a highly stereoselective manner. Further exploration with Sn(OTf)2 realized the rearrangement of a cross-aldehyde which tactically warrants the utility of the current approach to access complex polyketides. The origin of high stereoselectivity is attributed to a chairlike anti-conformation of the oxonium ion intermediate.

Cascade Michael addition/cycloketalization of cyclic 1,3-dicarbonyl compounds: important role of the tethered alcohol of α,β-unsaturated carbonyl compounds on reaction rate and regioselectivity.

Reactions of α,β-unsaturated aldehydes and cyclic 1,3-dicarbonyl compounds proceed primarily by cascade Knoevenagel condensation/six-π-electron electrocyclization (K6EC, formal [3 + 3] cycloaddition), while α,β-unsaturated ketones usually react with cyclic 1,3-dicarbonyl compounds in a 1,4-addition manner. This paper discloses our findings that under acidic conditions, α,β-unsaturated carbonyl compounds (ketones and aldehydes) with a tethered alcohol react with cyclic 1,3-dicarbonyl compounds in a highly regioselective 1,4-addition fashion via in situ generation of a hypothetical α-methylene cyclic oxonium ion as the reactive Michael acceptor. Our studies uncovered the important effect of the tethered alcohol on the reaction rate and/or efficiency and some new mechanistic aspects of the cascade Michael addition/cycloketalization. Finally, the substrate scope was examined, and 43 analogues of penicipyrone and tenuipyrone were prepared in good to excellent yields.

Synthesis of Polyketide Stereoarrays Enabled by a Traceless Oxonia‐Cope Rearrangement

AbstractPolyketide antibiotics bearing skipped polyols represent a synthetic challenge. A SiCl4‐promoted oxonia‐Cope rearrangement of syn,syn‐2‐vinyl‐1,3‐diols was developed to forge an array of 1,5‐pentenediols, thus providing versatile motifs for the preparation of 1,2,3,5‐stereoarrays in a highly stereoselective manner. Further exploration with Sn(OTf)2 realized the rearrangement of a cross‐aldehyde which tactically warrants the utility of the current approach to access complex polyketides. The origin of high stereoselectivity is attributed to a chairlike anti‐conformation of the oxonium ion intermediate.

O-Glycosylation of the N-terminal Region of the Serine-rich Adhesin Srr1 of Streptococcus agalactiae Explored by Mass Spectrometry

Serine-rich (Srr) proteins exposed at the surface of Gram-positive bacteria are a family of adhesins that contribute to the virulence of pathogenic staphylococci and streptococci. Lectin-binding experiments have previously shown that Srr proteins are heavily glycosylated. We report here the first mass-spectrometry analysis of the glycosylation of Streptococcus agalactiae Srr1. After Srr1 enrichment and trypsin digestion, potential glycopeptides were identified in collision induced dissociation spectra using X! Tandem. The approach was then refined using higher energy collisional dissociation fragmentation which led to the simultaneous loss of sugar residues, production of diagnostic oxonium ions and backbone fragmentation for glycopeptides. This feature was exploited in a new open source software tool (SpectrumFinder) developed for this work. By combining these approaches, 27 glycopeptides corresponding to six different segments of the N-terminal region of Srr1 [93-639] were identified. Our data unambiguously indicate that the same protein residue can be modified with different glycan combinations including N-acetylhexosamine, hexose, and a novel modification that was identified as O-acetylated-N-acetylhexosamine. Lectin binding and monosaccharide composition analysis strongly suggested that HexNAc and Hex correspond to N-acetylglucosamine and glucose, respectively. The same protein segment can be modified with a variety of glycans generating a wide structural diversity of Srr1. Electron transfer dissociation was used to assign glycosylation sites leading to the unambiguous identification of six serines and one threonine residues. Analysis of purified Srr1 produced in mutant strains lacking accessory glycosyltransferase encoding genes demonstrates that O-GlcNAcylation is an initial step in Srr1 glycosylation that is likely required for subsequent decoration with Hex. In summary, our data obtained by a combination of fragmentation mass spectrometry techniques associated to a new software tool, demonstrate glycosylation heterogeneity of Srr1, characterize a new protein modification, and identify six glycosylation sites located in the N-terminal region of the protein.

A dissociative quantum mechanical/molecular mechanical molecular dynamics simulation and infrared experiments reveal characteristics of the strongly hydrolytic arsenic(III).

This work presents a hybrid ab initio quantum mechanical/molecular mechanical simulation at the RI-MP2 level of theory investigating the hydrolysis process of arsenic(III), ultimately leading to arsenous acid (H3AsO3). A newly implemented dissociative water model has been applied to treat the interactions in the classical region, which is capable of describing non-neutral water species such as hydroxide and oxonium ions. Three stages of hydrolysis have been observed during the simulation and besides profound dynamical considerations, detailed insights into structural changes and atomic partial charge shifts are presented. In particular, the geometrical properties of H-bonds involved in each of the three proton transfer events and subsequent proton hopping reactions are discussed. A Laguerre tessellation analysis has been employed to estimate the molecular volume of H3AsO3. Estimations of pKa values of the arsenic(III)-aquo-complexes have been obtained at the G4 and CBS-Q//B3 levels of theory using a thermodynamic cycle, whereas rate constants for the final hydrolysis step have been determined via reaction path optimization and transition state theory. Newly recorded Fourier transform infrared (FT-IR) spectroscopy measurements have been compared to power spectra obtained from the simulation data, confirming its quality. The simulation findings, as well as results from computational spectroscopic calculations utilizing the PT2-VSCF methodology, proved valuable for the interpretation of the experimental FT-IR data, elucidating the particularities of the strongly observed IR Raman noncoincidence effect.

Gold(III) chloride catalyzed synthesis of chiral substituted 3-formyl furans from carbohydrates: application in the synthesis of 1,5-dicarbonyl derivatives and furo[3,2-c]pyridine.

This report describes a gold(III)-catalyzed efficient general route to densely substituted chiral 3-formyl furans under extremely mild conditions from suitably protected 5-(1-alkynyl)-2,3-dihydropyran-4-one using H2 O as a nucleophile. The reaction proceeds through the initial formation of an activated alkyne-gold(III) complex intermediate, followed by either a domino nucleophilic attack/anti-endo-dig cyclization, or the formation of a cyclic oxonium ion with subsequent attack by H2 O. To confirm the proposed mechanistic pathway, we employed MeOH as a nucleophile instead of H2 O to result in a substituted furo[3,2-c]pyran derivative, as anticipated. The similar furo[3,2-c]pyran skeleton with a hybrid carbohydrate-furan derivative has also been achieved through pyridinium dichromate (PDC) oxidation of a substituted chiral 3-formyl furan. The corresponding protected 5-(1-alkynyl)-2,3-dihydropyran-4-one can be synthesized from the monosaccharides (both hexoses and pentose) following oxidation, iodination, and Sonogashira coupling sequences. Furthermore, to demonstrate the potentiality of chiral 3-formyl furan derivatives, a TiBr4 -catalyzed reaction of these derivatives has been shown to offer efficient access to 1,5-dicarbonyl compounds, which on treatment with NH4 OAc in slightly acidic conditions afforded substituted furo[3,2-c]pyridine.

Structure Determination of Sucrose by Acetylation and Acid Hydrolysis

For the structure determination of D-(+)-sucrose, which consists of <TEX>${\alpha}$</TEX>-D-(+)-glucose and <TEX>${\beta}$</TEX>-D-(+)-fructose, it was acetylated with acetic anhydride and triethyl amine, pyridine, zinc chloride, and sodium acetate as catalysts. The acetylated D-(+)-sucrose was acid-hydrolyzed using sulfuric acid and sodium chloride in methanolic solution. The structures of the reaction products were determined by <TEX>$^1H$</TEX>-NMR and <TEX>$^{13}C$</TEX>-NMR spectra. The yield of the acetylation indicated the high value in zinc chloride as 70% in zinc chloride catalyst. The acid-hydrolyzed product of the acetylated D-(+)-sucrose, 2,3,4,6,1',3',4',6'-octa-O-acetyl-D-(+)-sucrose, gave 2,3,4,6-tetra-O-acetyl-<TEX>${\beta}$</TEX>-D-(+)-glucose and it suggests that the acetylated D-(+)-sucrose was rearranged through the formation of oxonium ion by mutarotation in the 2,3,4,6-tetra-O-acetyl-<TEX>${\alpha}$</TEX>-D-(+)-glucose moiety and through the ring opening in the 1',3',4',6'-tetra-O-acetyl-<TEX>${\beta}$</TEX>-D-(+)-fructose moiety.

Oxonium Ions Substituting Cesium Ions in the Structure of the New High‐Pressure Borate HP‐Cs1−x(H3O)xB3O5 (x=0.5–0.7)

The new high-pressure borate HP-Cs1-x (H3 O)x B3 O5 (x=0.5-0.7) was synthesized under high-pressure/high-temperature conditions of 6 GPa/900 °C in a Walker-type multianvil apparatus. The compound crystallizes in the monoclinic space group C2/c (Z=8) with the parameters a=1000.6(2), b=887.8(2), c=926.3(2) pm, β=103.1(1)°, V=0.8016(3) nm(3) , R1=0.0452, and wR2=0.0721 (all data). The boron-oxygen network is analogous to those of the compounds HP-MB3 O5 , (M=K, Rb) and exhibits all three structural motifs of borates-BO3 groups, corner-sharing BO4 tetrahedra, and edge-sharing BO4 tetrahedra-at the same time. Channels inside the boron-oxygen framework contain the cesium and oxonium ions, which are disordered on a specific site. Estimating the amount of hydrogen by solid-state NMR spectroscopy and X-ray diffraction led to the composition HP-Cs1-x (H3 O)x B3 O5 (x=0.5-0.7), which implies a nonzero phase width.

Characterization of intact N- and O-linked glycopeptides using higher energy collisional dissociation

Simultaneous elucidation of the glycan structure and the glycosylation site are needed to reveal the biological function of protein glycosylation. In this study, we employed a recent type of fragmentation termed higher energy collisional dissociation (HCD) to examine fragmentation patterns of intact glycopeptides generated from a mixture of standard glycosylated proteins. The normalized collisional energy (NCE) value for HCD was varied from 30 to 60% to evaluate the optimal conditions for the fragmentation of peptide backbones and glycoconjugates. Our results indicated that HCD with lower NCE values preferentially fragmented the sugar chains attached to the peptides to generate a ladder of neutral loss of monosaccharides, thereby enabling the putative glycan structure characterization. In addition, detection of the oxonium ions enabled unambiguous differentiation of glycopeptides from non-glycopeptides. In contrast, HCD with higher NCE values preferentially fragmented the peptide backbone and, thus, provided information needed for confident peptide identification. We evaluated the HCD approach with alternating NCE parameters for confident characterization of intact N- and O-linked glycopeptides in a single liquid chromatography–tandem mass spectrometry (LC–MS/MS) analysis. In addition, we applied a novel data analysis pipeline, so-called GlycoFinder, to form a basis for automated data analysis. Overall, 38 unique intact glycopeptides corresponding to eight glycosylation sites (six N-linked and two O-linked sites) were confidently identified from a standard protein mixture. This approach provided concurrent characterization of both the peptide and the glycan, thereby enabling comprehensive structural characterization of glycoproteins in a single LC–MS/MS analysis.

Confusing Quantitative Descriptions of BrønstedLowry AcidBase Equilibria in Chemistry Textbooks – A Critical Review and Clarifications for Chemical Educators

AbstractIn chemistry textbooks, the pK value of water in the solvent water at 25 °C is sometimes given as 14.0, sometimes as 15.7. This is confusing. The particular chemical reaction considered is the one in which water as BrønstedLowry acid reacts with water as BrønstedLowry base in water as solvent to yield equal concentrations of hydrated oxonium and hydroxide ions, H3O+(aq) and HO−(aq), respectively. This reaction is also known as the ‘self‐ionization’ of water for which the equilibrium constant is abbreviated as Kw with its known value of 10−14.0 at 25 °C, i.e., pKw(25 °C)=14.0. Identical values for pK and pKw at a fixed temperature appear reasonable, since K and Kw refer to one and the same reaction. Therefore, reasons for the apparent disagreement between the ‘thermodynamically correct’ pKa value for water (14.0 at 25 °C) and the value reported in most organic chemistry textbooks (15.7) should be discussed when teaching acidbase chemistry. There are good arguments for introducing, from the very beginning, the concepts of activity and thermodynamic standard states when teaching quantitative aspects of chemical equilibria. This also explains in a straightforward way why all thermodynamic equilibrium constants, including Kw, are dimensionless, and why pK(25 °C)=0.

N- and O-Glycosylation in the Murine Synaptosome

We present the first large scale study characterizing both N- and O-linked glycosylation in a site-specific manner on hundreds of proteins. We demonstrate that a lectin-affinity fractionation step using wheat germ agglutinin enriches not only peptides carrying intracellular O-GlcNAc, but also those bearing ER/Golgi-derived N- and O-linked carbohydrate structures. Liquid chromatography-MS (LC/MS) analysis with high accuracy precursor mass measurements and high sensitivity ion trap electron-transfer dissociation (ETD) were utilized for structural characterization of glycopeptides. Our results reveal both the identity of the precise sites of glycosylation and information on the oligosaccharide structures possible on these proteins. We report a novel iterative approach that allowed us to interpret the ETD data set directly without making prior assumptions about the nature and distribution of oligosaccharides present in our glycopeptide mixture. Over 2500 unique N- and O-linked glycopeptides were identified on 453 proteins. The extent of microheterogeneity varied extensively, and up to 19 different oligosaccharides were attached at a given site. We describe the presence of the well-known mucin-type structures for O-glycosylation, an EGF-domain-specific fucosylation and a rare O-mannosylation on the transmembrane phosphatase Ptprz1. Finally, we identified three examples of O-glycosylation on tyrosine residues.

Emulsion Condensation Polymerization in Dispersed Aqueous Media. Interfacial Reactions and Nanoparticle Formation

The polycondensation of polyesters from C12 monomers at 95 °C in aqueous o/w emulsions, stabilized by acidic surfactants, has been studied in detail with a range of methods during the course of the reaction, resulting in a better understanding of the underlying reaction mechanisms. Comparisons of different surfactants, and effects of added NaCl, demonstrate that the reaction site is located at the interface between the hydrophobic core of the emulsion droplets and the surrounding water and that the reaction rate is dependent on the local concentration of oxonium ions at the reaction site. The equilibrium conversion achieved at long reaction times is, however, independent of the choice of surfactant or addition of salt, and the state of thermodynamic equilibrium is discussed thoroughly. Interestingly, a fraction of numerous “nanoparticles” (droplets in the size range ≤100 nm) have been found to develop in addition to the original fraction of droplets in the 10 μm size range. It is suggested that these nanoparticles are formed when monomers dissolved in the aqueous phase undergo an acid-catalyzed reaction to generate water-insoluble oligomers. Once the nanoparticles are formed, the reactions in them proceed with a reaction mechanism similar to emulsion polymerization.

Stereoselective Synthesis of Oxa‐Bowls by Nucleophilic Addition to Oxonium Ions: Observation of Nucleophile‐Dependent Hydride Migration

AbstractA simple and reliable platform was developed for the synthesis of symmetrical oxa‐bowls through the Lewis acid mediated etherification of dimethyl acetals. An intramolecular hydride transfer was observed with the use of electron‐rich aryl nucleophiles, which also gave access to unsymmetrical oxa‐bowls.

Lactobacillus plantarum WCFS1 O-linked protein glycosylation: An extended spectrum of target proteins and modification sites detected by mass spectrometry

It has recently been shown that the major autolysin Acm2 from Lactobacillus plantarum WCFS1 undergoes intracellular O-GlcNAcylation [Fredriksen L, Mathiesen G, Moen A, Bron PA, Kleerebezem M, Eijsink VG, Egge-Jacobsen W. 2012. The major autolysin Acm2 from Lactobacillus plantarum undergoes cytoplasmic O-glycosylation. J Bacteriol. 194(2):325-333]. To gain more insight into the occurrence of this protein modification, methods based on the higher energy collisional fragmentation of the Orbitrap XL mass spectrometer to generate both diagnostic oxonium (glycan) ions and significant peptide sequencing information were used to detect and identify novel glycoproteins. This led to the identification of 10 novel glycoproteins, including four proteins with well-known functions in the cytoplasm, a compartment not previously recognized to contain glycosylated proteins in bacteria: the molecular chaperone DnaK, the E2 subunit of the pyruvate dehydrogenase complex PdhC, the signal recognition particle receptor FtsY and the DNA translocase FtsK1. Among the other, glycosylated proteins were two extracellular peptidoglycan hydrolases and a mucus-binding protein. In total, 49 glycosylation sites for N-acetylhexosamine (HexNAc) were detected in the 11 Lactobacillus glycoproteins found so far. Most of the attached glycans consisted of a single HexNAc per site, whereas hexose moieties were also found in a few cases (in both of the peptidoglycan hydrolases and in DnaK).

Molecular Dynamics Study of Oxygen Permeation of Ionomer of Hydrocarbon

Polymer electrolyte fuel cell (PEFC) is focused worldwide as the energy conversion device for next generation. However, it has never been popular because of high price and low efficiency. In cathode catalyst layer of polymer electrolyte fuel cell, an ionomer with which the catalyst is covered is very important on the point of transferring protons to the catalytic surface on the cathode side. On the other hand, it is said that ionomer interferes with oxygen permeation to the catalytic surface. The mechanism of oxygen permeation through the ionomer was not analyzed in detail because it is too small to research by experiment. In this research, we constructed the system including polymer electrolyte membrane, water molecule, oxonium ion and platinum surface by using molecular dynamics study, and researched about the effect of the water content of the ionomer on the structure of the ionomer and oxygen permeability.