Oxonium Ion Research Articles

Oxidative Deamination of N-Acetyl Neuraminic Acid: Substituent Effects and Mechanism.

A study of the mechanism of the oxidative deamination of the N-nitroso-N-acetyl sialyl glycosides leading with overall retention of configuration to the corresponding 2-keto-3-deoxy-D-glycero-D-galacto-nonulopyranosidonic acid (KDN) glycosides is described, making use of a series of differentially O-protected N-nitroso-N-acetyl sialyl glycosides and of isotopic labeling studies. No evidence is found for stereodirecting participation by ester groups at the 4- and 7-positions. Comparisons are drawn with oxidative deamination reactions of 4-amino-4-deoxy and 2-amino-2-deoxy hexopyranosides and a common mechanism is formulated involving the intermediacy of 1-oxabicyclo[3.1.0]hexyl oxonium ions following participation by the pyranoside ring oxygen. A minor reaction pathway has been uncovered by labeling studies in the β-thiosialosides that results in the exchange of the 4-O-acetyl group by the glacial acetic acid that serves as external nucleophile in the general oxidative deamination process. A mechanism is proposed for this exchange involving participation by the thioglycoside at the level of an intermediate diazoalkane.

Charge-Compensated Metallacarborane Building Blocks for Conjugation with Peptides.

The cobalt bis(dicarbollide) complex [commo-3,3'-Co(1,2-C2 B9 H11 )2 ](-) has captured much attention in biochemical and medical contexts, in particular for the treatment of tumors by boron neutron capture therapy (BNCT). Derivatives of cobalt bis(dicarbollide) are commonly prepared through ring-opening reactions of cyclic oxonium ions, so the corresponding products are usually charged. Furthermore, attempts to incorporate cobalt bis(dicarbollide) into peptides are rare, despite obvious potential advantages. Here the synthesis of an imidazolium-based charge-compensated cobalt bis(dicarbollide) building block, which allows additional modifications with moieties of biochemical relevance, such as monosaccharides, is reported. Furthermore, conjugates of these building blocks with the Y1 -receptor-selective derivative of neuropeptide Y ([F(7) ,P(34) ]-NPY) retained excellent response to hY1 receptors found to be overexpressed in breast tumors and metastases.

Convergent Synthesis of 2-Aryl-Substituted Quinolines by Gold-Catalyzed Cascade Reaction.

Gold-catalyzed auto-tandem catalysis has been developed for synthesizing 2-aryl-substituted quinolines. The reaction of an aniline bearing an acetal moiety with an aryl alkyne proceeded via formal [4+2]-cycloaddition, which involved the addition of gold acetylide to an oxonium ion to give amino alkyne intermediate and sequential 6-endo-dig cyclization of amino alkyne intermediate by attacking of nitrogen to alkyne moiety activated by gold catalyst. The cationic gold catalyst promoted two different processes by enhancing the nucleophilicity and electrophilicity of alkyne. This convergent synthetic methodology enabled the synthesis of a variety of 2-aryl-substituted quinolines.

Distinctive MS/MS Fragmentation Pathways of Glycopeptide-Generated Oxonium Ions Provide Evidence of the Glycan Structure.

Post-translational glycosylation of proteins play key roles in cellular processes and the site-specific characterisation of glycan structures is critical to understanding these events. Given the challenges regarding identification of glycan isomers, glycoproteomic studies generally rely on the assumption of conserved biosynthetic pathways. However, in a recent study, we found characteristically different HexNAc oxonium ion fragmentation patterns that depend on glycan structure. Such patterns could be used to distinguish between glycopeptide structural isomers. To acquire a mechanistic insight, deuterium-labelled glycopeptides were prepared and analysed. We found that the HexNAc-derived m/z 126 and 144 oxonium ions, differing in mass by H2 O, had completely different structures and that high-mannose N-glycopeptides generated abundant Hex-derived oxonium ions. We describe the oxonium ion decomposition mechanisms and the relative abundance of oxonium ions as a function of collision energy for a number of well-defined glycan structures, which provide important information for future glycoproteomic studies.

Comprehensive analysis of flagellin glycosylation in Campylobacter jejuni NCTC 11168 reveals incorporation of legionaminic acid and its importance for host colonization.

Campylobacter jejuni is the leading cause of bacterial gastroenteritis. It relies on several virulence factors for host colonization, including glycosylated flagella. C. jejuni NCTC 11168 modifies its flagellins with pseudaminic acid derivatives. It is also presumed to modify these proteins with legionaminic acid, although no glycopeptide evidence was available at the onset of this study. The enzyme encoded by cj1319 can be used to make legionaminic acid in vitro, but the pathway for legionaminic acid synthesis partially inferred by knockout mutagenesis in Campylobacter coli VC167 excludes Cj1319. To address this contradiction, we examined the presence of legionaminic acid in flagellin glycopeptides of wild-type (WT) C. jejuni NCTC 11168 and of a cj1319 knockout mutant. We used high-energy collision-induced dissociation to obtain amino acid sequences while also visualizing signature sugar oxonium ions. Data analysis was performed with PEAKS software, and spectra were manually inspected for glycopeptide determination and verification. We showed that legionaminic acid is present on the flagellins of C. jejuni NCTC 11168 and that flagellin glycosylation is highly heterogeneous, with up to six different sugars singly present at a given site. We found that the cj1319 mutant produces more legionaminic acid than WT, thus excluding the requirement for Cj1319 for legionaminic acid synthesis. We also showed that this mutant has enhanced chicken colonization compared with WT, which may in part be attributed to the high content of legionaminic acid on its flagella.

ChemInform Abstract: A Cascade Approach to Naphthalene Derivatives from o‐Alkynylbenzaldehydes and Enolizable Ketones via in‐situ‐Formed Acetals.

Using the in-situ-formed acetal strategy, a facile approach has been developed to synthesize naphthalene derivatives from o-alkynylbenzaldehydes and enolizable ketones. In situ acetal formation assists the condensation between o-alkynylbenzaldehydes and enolizable ketones to give chalcone derivatives under Bronsted acidic conditions. In situ acetal formation facilitates the reaction by increasing the electrophilicity of the carbonyl carbon of the o-alkynylaldehyde through oxonium ion formation, and also by enhancing the nucleophilicity of the α carbon of the ketone through the formation of an enol ether. The formed chalcones undergo trans to cis isomerization to effect alkyne–carbonyl metathesis to give naphthalene derivatives.

Substrate-Controlled Asymmetric Total Syntheses of Microcladallenes A, B, and C Based on the Proposed Structures.

Substrate-controlled asymmetric total syntheses of (+)-microcladallenes A, B, and C have been accomplished based on the proposed structures. The syntheses of microcladallenes A and B confirmed the structures and absolute configurations of both natural products. However, the synthesis of microcladallene C, which includes seven stereogenic centers and an (R)-bromoallene in its compact C15 framework, brought the realization that its proposed structure must be revised. The introduction of C12-bromine into these natural products with retention of configuration relied on TiBr4 -mediated nucleophile-assisting leaving group brominations, the stereochemical outcome of which could be attributed, at least in part, to an oxonium or halonium ion formation-fragmentation sequence through intricate neighboring group participation. In addition, the pivotal β-oriented vicinal cis-dichloride function in microcladallene C was elaborated through a novel tandem Cl2 -induced electrophilic cyclization/imidate chlorination process. The positive rotations of these natural products with an (R)-bromoallene constitute exceptions to Lowe's rule for reasons yet to be determined.

Extended O-GlcNAc on HLA Class-I-Bound Peptides.

We report unexpected mass spectrometric observations of glycosylated human leukocyte antigen (HLA) class I-bound peptides. Complemented by molecular modeling, in vitro enzymatic assays, and oxonium ion patterns, we propose that the observed O-linked glycans carrying up to five monosaccharides are extended O-GlcNAc's rather than GalNAc-initiated O-glycans. A cytosolic O-GlcNAc modification is normally terminal and does not extend to produce a polysaccharide, but O-GlcNAc on an HLA peptide presents a special case because the loaded HLA class I complex traffics through the endoplasmic reticulum and Golgi apparatus on its way to the cell membrane and is hence exposed to glycosyltransferases. We also report for the first time natural HLA class I presentation of O- and N-linked glycopeptides derived from membrane proteins. HLA class I peptides with centrally located oligosaccharides have been shown to be immunogenic and may thus be important targets for immune surveillance.

Kinetic and Mechanistic Studies of the Polymerization of Isobutylene Catalyzed by EtAlCl2/Bis(2-chloroethyl) Ether Complex in Hexanes

The kinetics and mechanism of the polymerization of isobutylene (IB) initiated by tert-butyl chloride and catalyzed by ethylaluminum dichloride (EADC)•bis(2-chloroethyl) ether (CEE) complex was studied in hexanes at 0 °C. The polymerization is first order in [IB] and in dry hexanes the slopes of the first order plots are independent of the [CEE]/[EADC] ratio in the range 1–1.5. From the slopes the steady state concentration of propagating cations [Mn+] = 1.8 × 10–11 M was calculated, which suggests an equilibrium between dormant and active species. The olefin distribution is independent of IB concentration and conversion. At low conversion, the number average molecular weight (Mn) is proportional to the starting IB concentration. In hexanes saturated with water, the polymerization rate is 5 times higher at [CEE]/[EADC] = 1 compared to that in dry hexanes. However, at [CEE]/[EADC] = 1.5, the rates in dry or wet hexanes are identical. To account for the low concentration of active centers determined from the first order plots, an equilibrium between oxonium (dormant) and carbenium (active) ions is proposed. The existence of oxonium ions was confirmed by 1H NMR studies and by polymerizations initiated from preformed oxonium ions. While identical rates and olefin distributions were obtained using EADC solutions in hexanes or toluene to form the EADC·CEE complex at short reaction times, at long reaction times, the exo-olefin content decreased when EADC solution in toluene was used. This was attributed to a slow tert-butylation of toluene yielding 95% para isomer and the concomitant formation of AlCl3.

Cooperativity between Al Sites Promotes Hydrogen Transfer and Carbon-Carbon Bond Formation upon Dimethyl Ether Activation on Alumina.

The methanol-to-olefin (MTO) process allows the conversion of methanol/dimethyl ether into olefins on acidic zeolites via the so-called hydrocarbon pool mechanism. However, the site and mechanism of formation of the first carbon–carbon bond are still a matter of debate. Here, we show that the Lewis acidic Al sites on the 110 facet of γ-Al2O3 can readily activate dimethyl ether to yield CH4, alkenes, and surface formate species according to spectroscopic studies combined with a computational approach. The carbon–carbon forming step as well as the formation of methane and surface formate involves a transient oxonium ion intermediate, generated by a hydrogen transfer between surface methoxy species and coordinated methanol on adjacent Al sites. These results indicate that extra framework Al centers in acidic zeolites, which are associated with alumina, can play a key role in the formation of the first carbon–carbon bond, the initiation step of the industrial MTO process.

Syntheses, structures and catecholase activity of two cobalt(III) complexes derived from N,N′-ethylenebis(3-ethoxysalicylaldiimine): A special host–guest system from a special ligand

The work in this report deals with syntheses, crystal structures, catechol oxidase activity and ESI-MS (positive) studies of two mononuclear cobalt(III) compounds [CoIIILOEt–en(N3)2⊃(H3O+)]·2MeOH (1) and [CoIIILOEt–en(NCS)(H2O)]·DMF·H2O (2), where H2LOEt–en is N,N′-ethylenebis(3-ethoxysalicylaldiimine). The metal center in both the compounds occupies N(imine)2O(phenoxo)2 compartment. Two apical coordination positions are occupied by one anionic ligand (thiocyanate) and one neutral ligand (water) in 2 but by two anionic ligands (azide) in 1. The extra negative charge in [CoIIILOEt–en(N3)2]− is balanced by an oxonium ion (H3O+), which is trapped in the O(phenoxo)2O(ethoxy)2 compartment to result in the formation of host–guest species [CoIIILOEt–en(N3)2⊃(H3O+)] in 1. Both the compounds show catechol oxidase activity (1 in MeCN, 2 in DMF) as monitored by the UV–Vis spectroscopy of the aerial oxidation of 3,5-DTBCH2 to 3,5-DTBQ. The kinetic parameters have been determined using Michaelis–Menten approach. The Kcat values for 1 in MeCN and 2 in DMF are 10.0h−1 and 11.2h−1, respectively. ESI-MS (positive) of 1 and the mixture of 1 and 3,5-DTBCH2 have been recorded and the positive ions have been well assigned. Interestingly, a 1:2 adduct of composition [CoIILOEt–en(3,5-DTBQ)2+H+]+ has been identified from the spectrum of the mixture of 1 and 3,5-DTBCH2. Unique features of 1 and 2 in terms of showing catechol oxidase activity and, more importantly, unique structural features of compound 1 have been discussed.

A Cascade Approach to Naphthalene Derivatives from o‐Alkynylbenzaldehydes and Enolizable Ketones via in‐situ‐Formed Acetals

AbstractUsing the in‐situ‐formed acetal strategy, a facile approach has been developed to synthesize naphthalene derivatives from o‐alkynylbenzaldehydes and enolizable ketones. In situ acetal formation assists the condensation between o‐alkynylbenzaldehydes and enolizable ketones to give chalcone derivatives under Brønsted acidic conditions. In situ acetal formation facilitates the reaction by increasing the electrophilicity of the carbonyl carbon of the o‐alkynylaldehyde through oxonium ion formation, and also by enhancing the nucleophilicity of the α carbon of the ketone through the formation of an enol ether. The formed chalcones undergo trans to cis isomerization to effect alkyne–carbonyl metathesis to give naphthalene derivatives.

Exploration of weak interaction directed self-assemblies on reacting mononuclear copper(II)/nickel(II)⋯water host⋯guest systems of a double-compartment ligand with mono/di/tricarboxylic acids

The work in this report deals with the syntheses, characterization, molecular and supramolecular structures of eight compounds of the composition [{CuIILOEt–en⊂(H3O)}(o-chlorobenzoate)] (1), [{CuIILOEt–en⊂(H2O)}2(fumaric acid)] (2), [{NiIILOEt–en⊂(H2O)}2(fumaric acid)] (3), [{CuIILOEt–en⊂(H2O)}2(succinic acid)] (4), [{NiIILOEt–en⊂(H2O)}2(succinic acid)] (5), [{NiIILOEt–en⊂(H2O)}2(terephthalic acid)] (6), [{CuIILOEt–en⊂(H2O)}(1,3,5-benzenetricarboxylic acid)]·MeOH (7) and [{NiIILOEt–en⊂(H2O)}(1,3,5-benzenetricarboxylic acid)]·MeOH (8), where H2LOEt–en is N,N′-ethylenebis(3-ethoxysalicylaldimine). These compounds are obtained on reacting the mononuclear host–guest compound [CuIILOEt–en⊂(H2O)]/[NiIILOEt–en⊂(H2O)], which contains a trapped water molecule, with the corresponding mono/di/tricarboxylic acid. One water molecule in 2–8 and one oxonium ion in 1 is trapped in each O(phenoxo)2O(ethoxy)2 compartment. Both the carboxylic acid groups of the dicarboxylic acids are involved in interacting with the trapped water molecule, forming the supramolecular dimers 2–6, while one of the three carboxylic acid groups of 1,3,5-benzenetricarboxylic acid is involved in O–H⋯O(trapped water) hydrogen bond, forming the 1:1 adducts 7 and 8. Compound 1 contains o-chlorobenzoate and the trapped species herein is the oxonium ion (H3O+). [{CuIILOEt–en⊂(H3O)]+ and o-chlorobenzoate fragments in 1 are self-assembled because of an O–H(oxonium ion)⋯O(carboxylate) hydrogen bond. The above mentioned adducts are further self-assembled to generate 1-D/2-D/3-D supramolecular structures because of hydrogen bonds/π⋯π interactions/NiII⋯NiII interactions/halogen bonds.

GPQuest: A Spectral Library Matching Algorithm for Site-Specific Assignment of Tandem Mass Spectra to Intact N-glycopeptides.

Glycoprotein changes occur in not only protein abundance but also the occupancy of each glycosylation site by different glycoforms during biological or pathological processes. Recent advances in mass spectrometry instrumentation and techniques have facilitated analysis of intact glycopeptides in complex biological samples by allowing the users to generate spectra of intact glycopeptides with glycans attached to each specific glycosylation site. However, assigning these spectra, leading to identification of the glycopeptides, is challenging. Here, we report an algorithm, named GPQuest, for site-specific identification of intact glycopeptides using higher-energy collisional dissociation (HCD) fragmentation of complex samples. In this algorithm, a spectral library of glycosite-containing peptides in the sample was built by analyzing the isolated glycosite-containing peptides using HCD LC-MS/MS. Spectra of intact glycopeptides were selected by using glycan oxonium ions as signature ions for glycopeptide spectra. These oxonium-ion-containing spectra were then compared with the spectral library generated from glycosite-containing peptides, resulting in assignment of each intact glycopeptide MS/MS spectrum to a specific glycosite-containing peptide. The glycan occupying each glycosite was determined by matching the mass difference between the precursor ion of intact glycopeptide and the glycosite-containing peptide to a glycan database. Using GPQuest, we analyzed LC-MS/MS spectra of protein extracts from prostate tumor LNCaP cells. Without enrichment of glycopeptides from global tryptic peptides and at a false discovery rate of 1%, 1008 glycan-containing MS/MS spectra were assigned to 769 unique intact N-linked glycopeptides, representing 344 N-linked glycosites with 57 different N-glycans. Spectral library matching using GPQuest assigns the HCD LC-MS/MS generated spectra of intact glycopeptides in an automated and high-throughput manner. Additionally, spectral library matching gives the user the possibility of identifying novel or modified glycans on specific glycosites that might be missing from the predetermined glycan databases.

Transnitrosation of non-mutagenic N-nitrosoproline forms mutagenic N-nitroso-N-methylurea

N-Nitroso-N-methylurea (NMU) is a potent carcinogen and suspected as a cause of human cancer. In this study, mutagenic NMU was detected by HPLC after the transnitrosation of non-mutagenic N-nitrosoproline (NP) to N-methylurea in the presence of thiourea (TU) under acidic conditions. The structure of NMU was confirmed by comparing 1H NMR and IR spectra with that of authentic NMU after fractionation by column chromatography. Furthermore, a fraction containing NMU formed by transnitrosation was mutagenic in Salmonella typhimurium TA1535.NMU was formed in the reaction of NP and N-methylurea in the presence of 1,1,3,3-tetramethylthiourea (TTU) or 1,3-dimethylthiourea in place of TU as an accelerator. The reaction rate constants (k) for NMU formation were correlated with their nucleophilicity of sulfur atom in thioureas. The N-methylurea concentration did not affect the NMU formation, whereas the rate of NMU formation correlated linearly with concentrations of NP, TTU and oxonium ion. The observed kinetics suggests a mechanism by which the nitroso group was transferred directly from the protonated NP to the thiourea then to N-methylurea to form NMU. The rate-determining step was the formation of the complex with the protonated NP and thiourea.

Influence of alkoxy groups on rates of acetal hydrolysis and tosylate solvolysis: electrostatic stabilization of developing oxocarbenium ion intermediates and neighboring-group participation to form oxonium ions.

The hydrolysis of 4-alkoxy-substituted acetals was accelerated by about 20-fold compared to that of sterically comparable substrates that do not have an alkoxy group. Rate accelerations are largest when the two functional groups are linked by a flexible cyclic tether. When controlled for the inductive destabilization, an alkoxy group can accelerate acetal hydrolysis by up to 200-fold. The difference in rates of acetal hydrolysis between a substrate where the alkoxy group was tethered to the acetal group by a five-membered ring compared to one where it was tethered by an eight-membered ring was less than 100-fold, suggesting that fused-ring intermediates were not formed. By comparison, the difference in rates of solvolysis of structurally related tosylates were nearly 10(6)-fold between the five- and eight-membered ring series. This observation implicates neighboring-group participation in the solvolysis of tosylates but not in the hydrolysis of acetals. The acceleration of acetal hydrolysis by an alkoxy group is better explained by electrostatic stabilization of intermediates that accumulate positive charge at the acetal carbon atom.

Generation of stable carbocations in polydiphenylenesulfophthalide and ortho-substituted polytriarylcarbinols upon water desorption

Formation of “green” color centers (CCs) with two absorption bands (ABs) in the visible spectrum at 480 and 610 nm upon evacuation and/or weak heating (~100 °C) of films of polytriarylcarbinol (PTAC) and polydiphenylenesulfophthalide (PDSP) due to loss of sorbed water was observed. Electronic spectra (ES) of solutions of compounds that simulate polymers, PTAC and PDSP polymers in sulfuric acid were obtained. Isolated CCs having ABs in electronic spectra (ES) at 462 and 595 nm were generated by “slight” treatment of a PTAC film with sulfuric acid. The ES of a series of model carbocations and energies of ionization of the model triphenylcarbinols by proton, oxonium ion and Li+ ion were calculated in B3LYP/6-311G(d,p) approximation. Experimental and theoretical results are showed that the CCs in question are carbocation nature. The paper discusses the ionization mechanism in polymers and some aspects of heterogeneous (in water) and homogeneous (in organic polar solvent) methods of PTAC preparation.

ChemInform Abstract: 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.

ChemInform Abstract: 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.

Characterizing sialic acid variants at the glycopeptide level.

Beam-type collision-induced dissociation (CID) data of intact glycopeptides isolated from mouse liver tissue are presented to illustrate characteristic fragmentation of differentially sialylated glycopeptides. Eight glycoforms of an O-linked glycopeptide from Nucleobindin-1 are distinguished on the basis of the precursor masses and characteristic oxonium ions. We report that all sialic acid variants are prone to neutral loss from the charge reduced species in electron-transfer dissociation (ETD) fragmentation. We show how changes in sialic acid composition affect reverse phase chromatographic retention times: sialic acid addition increases glycopeptide retention times significantly; replacing the N-acetylneuraminic acid with the N-glycolyl variant leads to slightly reduced retention times, while O-acetylated sialic acid-containing glycoforms are retained longer. We then demonstrate how MS-Filter in Protein Prospector can use these diagnostic oxonium ions to find glycopeptides, by showing that a wealth of different glycopeptides can be found in a published phosphopeptide data set.