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Abstract Attaining complete anomeric control is still one of the biggest challenges in carbohydrate chemistry. Glycosyl cations such as oxocarbenium and dioxanium ions are key intermediates of glycosylation reactions. Characterizing these highly-reactive intermediates and understanding their glycosylation mechanisms are essential to the stereoselective synthesis of complex carbohydrates. Although C-2 acyl neighbouring-group participation has been well-studied, the reactive intermediates in more remote participation remain elusive and are challenging to study. Herein, we report a workflow that is utilized to characterize rhamnosyl 1,3-bridged dioxanium ions derived from C-3 p-anisoyl esterified donors. First, we use a combination of quantum-chemical calculations and infrared ion spectroscopy to determine the structure of the cationic glycosylation intermediate in the gas-phase. In addition, we establish the structure and exchange kinetics of highly-reactive, low-abundance species in the solution-phase using chemical exchange saturation transfer, exchange spectroscopy, correlation spectroscopy, heteronuclear single-quantum correlation, and heteronuclear multiple-bond correlation nuclear magnetic resonance spectroscopy. Finally, we apply C-3 acyl neighbouring-group participation to the synthesis of complex bacterial oligosaccharides. This combined approach of finding answers to fundamental physical-chemical questions and their application in organic synthesis provides a robust basis for elucidating highly-reactive intermediates in glycosylation reactions.

Abstract Modern untargeted mass spectrometry (MS) analyses quickly detect and resolve thousands of molecular compounds. Although features are readily annotated with a molecular formula in high-resolution small-molecule MS applications, the large majority of them remains unidentified in terms of their full molecular structure. Collision-induced dissociation tandem mass spectrometry (CID-MS2) provides a diagnostic molecular fingerprint to resolve the molecular structure through a library search. However, for de novo identifications, one must often rely on in silico generated MS2 spectra as reference. The ability of different in silico algorithms to correctly predict MS2 spectra and thus to retrieve correct molecular structures is a topic of lively debate, for instance in the CASMI contest. Underlying the predicted MS2 spectra are the in silico generated product ion structures, which are normally not used in de novo identification, but which can serve to critically assess the fragmentation algorithms. Here we evaluate in silico generated MSn product ion structures by comparison with structures established experimentally by infrared ion spectroscopy (IRIS). For a set of three dozen product ion structures from five precursor molecules, we find that virtually all fragment ion structure annotations in three major in silico MS2 libraries (HMDB, METLIN, mzCloud) are incorrect and caution the reader against their use for structure annotation of MS/MS ions.

Herein, we explore the generation and characterization of the radical cations of glycylphenylalanylglycine, or [GFG]•+, formed via dissociative electron-transfer reaction from the tripeptide to copper(II) within a ternary complex. A comprehensive investigation employing isotopic labeling, infrared multiple-photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations elucidated the details and energetics in formation of the peptide radical cations as well as their dissociation products. Unlike conventional aromatic-containing peptide radical cations that primarily form canonical π-radicals, our findings reveal that 75% of the population of the experimentally produced [GFG]•+ precursors are [GFα•G]+, where the radical resides on the middle α-carbon of the phenylalanyl residue. This unexpected isomeric ion has an enthalpy of 6.8 kcal/mol above the global minimum, which has an N-terminal captodative structure, [Gα•FG]+, comprising 25% of the population. The [b₂-H]•+ product ions are also present in a ratio of 75/25 from [GFα•G]+/ [Gα•FG]+, the results of which are obtained from matches between the IRMPD action spectrum and predicted IR absorption spectra of the [b₂-H]•+ candidate structures, as well as from IRMPD isomer population analyses.

Cored wire is a widespread technology used for performing additions into liquid metal baths as an alternative to bulk-additions. A laboratory-scale study was performed in which the kinetics of assimilation of cored wire in liquid steel baths were studied. An original dataset of positions of the wire/melt interface of cored wire as a function of the time and steel bath temperature was produced. The dataset was compared against results of simulations made with a transient 1D (radial) thermal model of the assimilation of cored wire, and demonstrated reasonable agreement. Hence, this paper provides a dataset that can be used as a resource for the validation of future developments in the field of modeling cored wire injection into liquid metal baths.

Combined metabolomics, NMR, and, IRIS identify biomarkers of hyperprolinemia type II (HPII) distinct from HPI and similar metabolic signatures as in patients with pyridoxine-dependent epilepsy.

We report experimental values for the CH stretch frequencies of the protonated fullerenes C _60 H ^+ and C _70 H ^+ . Anharmonic frequency calculations at the B3LYP/6-31G level of theory, which are independent of empirical scaling factors, reproduce the experimental values to within approximately 5 cm ^−1 . Scaling theoretical harmonic frequencies by applying factors derived for polycyclic aromatic hydrocarbons deviate significantly from the experimentally measured frequency. We attribute this deviation to the unusual hydrocarbon structure that affects the degree of anharmonicity of the CH stretch. This result allows us to propose an original, specific scaling factor of 0.9524 to correct harmonic frequencies of CH stretches of protonated fullerenes calculated at the B3LYP/6-311 + G(d,p) level of theory. The special spectral position of the protonated fullerene CH stretch bands makes it a diagnostic marker that may aid in their detection in the interstellar medium.

Glutathione is a biologically abundant and redox active tripeptide that serves to protect cells from oxidative stress and rid the body of toxic heavy metals. The present study examines the coordination complexes of glutathione (GSH) with metals that are central to redox processes in biology, Zn, Cu, and Fe, using infrared multiple photon dissociation (IRMPD) action spectroscopy with a free electron laser. For all three metals, a complex between the metal dication and deprotonated GSH was formed, M(GSHH)+. The experimental IRMPD spectra were compared to scaled harmonic vibrational spectra calculated at the MP2/6-311+G(d,p) level of theory after thorough exploration of conformational space using a simulated annealing protocol. Interestingly, spectra calculated at the B3LYP or oB97XD level do not match experiment as well. These findings offer the first gas-phase spectroscopic evidence for how the biologically relevant metal ions coordinate with glutathione. There are spectral features that are common to all three metals, however, noting the differences in the strengths of the common features between the three metals enables an assessment of the preference or specificity that each individual metal has for a given coordination site. Additionally, all three metals form structures where the deprotonated thiol of the cysteine side chain coordinates with the metal center, which is consistent with the involvement of the thiol site in biologically relevant redox chemistry. Introduction Glutathione (L-g-glutamyl-L-cysteinylglycine, GSH) is a biologically abundant tripeptide. [ABSTRACT FROM AUTHOR]

Infrared emission features are observed towards diverse astronomical objects in the interstellar medium (ISM). Generally, the consensus is that these IR features originate from polycyclic aromatic hydrocarbons (PAHs) and are hence named aromatic infrared bands (AIBs). More recently, it has been suggested that nitrogen substituted PAHs (PANHs) contribute to the AIBs as well and it has even been shown that nitrogen inclusion in PAHs can improve the match with the AIBs, specifically around the 6.2 μm feature. In order to determine which specific molecules or functional groups are at the origin of the AIBs, IR spectra of various PA(N)Hs are experimentally and computationally studied. In this work we expand on the spectroscopic investigation of PANHs by presenting the gas-phase mid-IR spectra of 1,5,9-triazacoronene˙+ (TAC˙+, m/z 303), a threefold nitrogenated congener of coronene˙+, its protonated derivative TACH+ (m/z 304) and the product that forms when water adds to dehydrogenated TAC˙+[TAC–H + H2O]+ (m/z 320). We analyze the mid-IR spectra by comparing them with vibrational modes calculated at the B3LYP/6-311++G(d,p) level a theory and we present a possible geometry for [TAC–H + H2O]+. The TAC˙+ mid-IR spectrum is compared to that of coronene˙+ and is demonstrated to be remarkably similar. We put TAC˙+ and TACH+ into astronomical context by comparing their recorded mid-IR spectra to observed ISM spectra of four spectral classes. From this we conclude that TAC˙+ and TACH+ could both contribute to the AIBs, with TACH+ being a more likely contributor than TAC˙+. [ABSTRACT FROM AUTHOR]

Herein, we explore the generation and characterization of the radical cations of glycylphenylalanylglycine, or [GFG]•+, formed via dissociative electron-transfer reaction from the tripeptide to copper(II) within a ternary complex. A comprehensive investigation employing isotopic labeling, infrared multiple-photon dissociation (IRMPD) spectroscopy, and density functional theory (DFT) calculations elucidated the details and energetics in formation of the peptide radical cations as well as their dissociation products. Unlike conventional aromatic-containing peptide radical cations that primarily form canonical π-radicals, our findings reveal that 75% of the population of the experimentally produced [GFG]•+ precursors are [GFα•G]+, where the radical resides on the middle α-carbon of the phenylalanyl residue. This unexpected isomeric ion has an enthalpy of 6.8 kcal/mol above the global minimum, which has an N-terminal captodative structure, [Gα•FG]+, comprising 25% of the population. The [b₂-H]•+ product ions are also present in a ratio of 75/25 from [GFα•G]+/ [Gα•FG]+, the results of which are obtained from matches between the IRMPD action spectrum and predicted IR absorption spectra of the [b₂-H]•+ candidate structures, as well as from IRMPD isomer population analyses. [ABSTRACT FROM AUTHOR]

Cored wire is a widespread technology used for performing additions into liquid metal baths as an alternative to bulk-additions. A laboratory-scale study was performed in which the kinetics of assimilation of cored wire in liquid steel baths were studied. An original dataset of positions of the wire/melt interface of cored wire as a function of the time and steel bath temperature was produced. The dataset was compared against results of simulations made with a transient 1D (radial) thermal model of the assimilation of cored wire, and demonstrated reasonable agreement. Hence, this paper provides a dataset that can be used as a resource for the validation of future developments in the field of modeling cored wire injection into liquid metal baths. [ABSTRACT FROM AUTHOR]

Attaining complete anomeric control is still one of the biggest challenges in carbohydrate chemistry. Glycosyl cations such as oxocarbenium and dioxanium ions are key intermediates of glycosylation reactions. Characterizing these highly-reactive intermediates and understanding their glycosylation mechanisms are essential to the stereoselective synthesis of complex carbohydrates. Although C-2 acyl neighbouring-group participation has been well-studied, the reactive intermediates in more remote participation remain elusive and are challenging to study. Herein, we report a workflow that is utilized to characterize rhamnosyl 1,3-bridged dioxanium ions derived from C-3 p-anisoyl esterified donors. First, we use a combination of quantum-chemical calculations and infrared ion spectroscopy to determine the structure of the cationic glycosylation intermediate in the gas-phase. In addition, we establish the structure and exchange kinetics of highly-reactive, low-abundance species in the solution-phase using chemical exchange saturation transfer, exchange spectroscopy, correlation spectroscopy, heteronuclear single-quantum correlation, and heteronuclear multiple-bond correlation nuclear magnetic resonance spectroscopy. Finally, we apply C-3 acyl neighbouring-group participation to the synthesis of complex bacterial oligosaccharides. This combined approach of finding answers to fundamental physical-chemical questions and their application in organic synthesis provides a robust basis for elucidating highly-reactive intermediates in glycosylation reactions. Characterizing highly-reactive glycosyl cation intermediates and understanding their glycosylation mechanisms are essential to the stereoselective synthesis of complex carbohydrates. Here the authors report a workflow that is utilized to characterize rhamnosyl 1,3-bridged dioxanium ions derived from C-3 p-anisoyl esterified donors. [ABSTRACT FROM AUTHOR]

Modern untargeted mass spectrometry (MS) analyses quickly detect and resolve thousands of molecular compounds. Although features are readily annotated with a molecular formula in high-resolution small-molecule MS applications, the large majority of them remains unidentified in terms of their full molecular structure. Collision-induced dissociation tandem mass spectrometry (CID-MS2) provides a diagnostic molecular fingerprint to resolve the molecular structure through a library search. However, for de novo identifications, one must often rely on in silico generated MS2 spectra as reference. The ability of different in silico algorithms to correctly predict MS2 spectra and thus to retrieve correct molecular structures is a topic of lively debate, for instance in the CASMI contest. Underlying the predicted MS2 spectra are the in silico generated product ion structures, which are normally not used in de novo identification, but which can serve to critically assess the fragmentation algorithms. Here we evaluate in silico generated MSn product ion structures by comparison with structures established experimentally by infrared ion spectroscopy (IRIS). For a set of three dozen product ion structures from five precursor molecules, we find that virtually all fragment ion structure annotations in three major in silico MS2 libraries (HMDB, METLIN, mzCloud) are incorrect and caution the reader against their use for structure annotation of MS/MS ions. Collision-induced dissociation tandem mass spectrometry offers to resolve molecular structures through library searches, however, for de novo identifications, one must often rely on in silico-generated spectra as reference. Here, the authors evaluate in silico generated MSn product ion structures by comparison with spectroscopically established structures and find that for 36 randomly selected MS/MS product ions, the vast majority of annotations in three major libraries are incorrect, primarily due to unaccounted for cyclization rearrangements. [ABSTRACT FROM AUTHOR]

Proton and hydrogen-bonded networks sustain a broad range of structural and charge transfer processes in supramolecular materials. The modelling of proton dynamics is however challenging and demands insights from prototypical benchmark systems. The intramolecular H-bonding networks induced by either protonation or deprotonation of 3-hydroxyglutaric acid provide intriguing case studies of correlated proton dynamics. The vibrational signatures associated with the fluxional proton bonding and its coupling with the hydroxyglutaric backbone are investigated here with infrared action ion spectroscopy experiments and Born–Oppenheimer molecular dynamics (BOMD) computations. Despite the formally similar symmetry of protonated and deprotonated hydroxyglutaric acid, the relative proton affinities of the oxygen centers of the carboxylic and carboxylate groups with respect to that of the central hydroxyl group lead to distinct proton dynamics. In the protonated acid, a tautomeric arrangement of the type HOCO·[HOH]+·OCOH is preferred with the proton binding tighter to the central hydroxyl moiety and the electronic density being shared between the two nearly symmetric H-bonds with the carboxylic end groups. In the deprotonated acid, the asymmetric [OCO]−·HO·HOCO configuration is more stable, with a stronger H-bonding on the bare carboxylate end. Both systems display active backbone dynamics and concerted Grothuss-like proton motions, leading to diffuse band structures in their vibrational spectra. These features are accurately reproduced by the BOMD computations. [ABSTRACT FROM AUTHOR]

Intramolecular radical and proton migration in the gas phase are important processes driving the dissociation reactions underlying common tandem mass spectrometry processes, such as collision-induced and electron-induced dissociation reactions (CID and ExD). Mechanistic insights in these processes requires experiments that probe the molecular structures of ions along the reaction pathways, usually combined with quantum-chemical calculations. The combination of ion trap mass spectrometry with IR laser spectroscopy, pioneered among others by Dieter Gerlich, provides a particularly effective method to explore details of the ion structures. In this work, we employ infrared multiple-photon dissociation (IRMPD) spectroscopy and density functional theory (DFT) calculations to probe the reactant and product ion structures of a homolytic bond cleavage reaction. First, we employ IRMPD spectroscopy to establish that protonation of the 4-bromoaniline precursor occurs on the amine moiety and then that C-Br homolytic cleavage produces the π-radical cation of aniline. Transition-state calculations are performed to compare the various pathways that connect reactant and product ions, including both proton and radical transfer mechanisms. [ABSTRACT FROM AUTHOR]

The identification of biotransformation products of drug compounds is a crucial step in drug development. Over the last decades, liquid chromatography‐mass spectrometry (LC‐MS) has become the method of choice for metabolite profiling because of its high sensitivity and selectivity. However, determining the full molecular structure of the detected metabolites, including the exact biotransformation site, remains challenging on the basis of MS alone. Here we explore infrared ion spectroscopy (IRIS) as a novel MS‐based method for the elucidation of metabolic pathways in drug metabolism research. Using the drug midazolam as an example, we identify several biotransformation products directly from an in vitro drug incubation sample. We show that IR spectra of the aglycone MS/MS fragment ions of glucuronide metabolites establish a direct link between detected phase I and phase II metabolites. Moreover, using quantum‐chemically computed IR spectra of candidate structures, we are able to assign the exact sites of biotransformation in absence of reference standards. Additionally, we demonstrate the utility of IRIS for structural elucidation by identifying several ring‐opened midazolam derivatives formed in an acidic environment. [ABSTRACT FROM AUTHOR]

We used next‐generation metabolic screening to identify new biomarkers for improved diagnosis and pathophysiological understanding of glucose transporter type 1 deficiency syndrome (GLUT1DS), comparing metabolic cerebrospinal fluid (CSF) profiles from 12 patients to those of 116 controls. This confirmed decreased CSF glucose and lactate levels in patients with GLUT1DS and increased glutamine at group level. We identified three novel biomarkers significantly decreased in patients, namely gluconic + galactonic acid, xylose‐α1‐3‐glucose, and xylose‐α1‐3‐xylose‐α1‐3‐glucose, of which the latter two have not previously been identified in body fluids. CSF concentrations of gluconic + galactonic acid may be reduced as these metabolites could serve as alternative substrates for the pentose phosphate pathway. Xylose‐α1‐3‐glucose and xylose‐α1‐3‐xylose‐α1‐3‐glucose may originate from glycosylated proteins; their decreased levels are hypothetically the consequence of insufficient glucose, one of two substrates for O‐glucosylation. Since many proteins are O‐glucosylated, this deficiency may affect cellular processes and thus contribute to GLUT1DS pathophysiology. The novel CSF biomarkers have the potential to improve the biochemical diagnosis of GLUT1DS. Our findings imply that brain glucose deficiency in GLUT1DS may cause disruptions at the cellular level that go beyond energy metabolism, underlining the importance of developing treatment strategies that directly target cerebral glucose uptake. [ABSTRACT FROM AUTHOR]

Uronic acids are carbohydrates carrying a terminal carboxylic acid and have a unique reactivity in stereoselective glycosylation reactions. Herein, the competing intramolecular stabilization of uronic acid cations by the C‐5 carboxylic acid or the C‐4 acetyl group was studied with infrared ion spectroscopy (IRIS). IRIS reveals that a mixture of bridged ions is formed, in which the mixture is driven towards the C‐1,C‐5 dioxolanium ion when the C‐5,C‐2‐relationship is cis, and towards the formation of the C‐1,C‐4 dioxepanium ion when this relation is trans. Isomer‐population analysis and interconversion barrier computations show that the two bridged structures are not in dynamic equilibrium and that their ratio parallels the density functional theory computed stability of the structures. These studies reveal how the intrinsic interplay of the different functional groups influences the formation of the different regioisomeric products. [ABSTRACT FROM AUTHOR]

Hyperprolinemia type II (HPII) is an inborn error of metabolism due to genetic variants in ALDH4A1, leading to a deficiency in Δ-1-pyrroline-5-carboxylate (P5C) dehydrogenase. This leads to an accumulation of toxic levels of P5C, an intermediate in proline catabolism. The accumulating P5C spontaneously reacts with, and inactivates, pyridoxal 5'-phosphate, a crucial cofactor for many enzymatic processes, which is thought to be the pathophysiological mechanism for HPII. Here, we describe the use of a combination of LC-QTOF untargeted metabolomics, NMR spectroscopy and infrared ion spectroscopy (IRIS) to identify and characterize biomarkers for HPII that result of the spontaneous reaction of P5C with malonic acid and acetoacetic acid. We show that these biomarkers can differentiate between HPI, caused by a deficiency of proline oxidase activity, and HPII. The elucidation of their molecular structures yields insights into the disease pathophysiology of HPII. Combined metabolomics, NMR, and, IRIS identify biomarkers of hyperprolinemia type II (HPII) distinct from HPI and similar metabolic signatures as in patients with pyridoxine-dependent epilepsy. [ABSTRACT FROM AUTHOR]

N‐Acyliminium ions are highly reactive intermediates that are important for creating CC‐bonds adjacent to nitrogen atoms. Here we report the characterization of cyclic N‐acyliminium ions in the gas phase, generated by collision induced dissociation tandem mass spectrometry followed by infrared ion spectroscopy using the FELIX infrared free electron laser. Comparison of DFT calculated spectra with the experimentally observed IR spectra provided valuable insights in the conformations of the N‐acyliminium ions. [ABSTRACT FROM AUTHOR]