Characterization of Elusive Reaction Intermediates Using Infrared Ion Spectroscopy: Application to the Experimental Characterization of Glycosyl Cations

Real-time capture of reactive intermediates in an enzymatic reaction: insights into a P450-catalyzed oxidation

Enzymes are indispensable for a myriad of biochemical reactions in nature. Although rapid spectroscopic techniques and operando methods allow for real-time assessment of enzyme kinetics, isolating and identifying the reactive intermediates in enzymatic reactions remains a significant challenge. These intermediates often possess fleeting lifespans, prohibiting their direct detection. This study harnessed online mass spectrometric techniques and microfluidic sampling methods to monitor the formation of reactive intermediates in real time during enzymatic catalysis in vitro. Using CYP175A1, a thermophilic P450 enzyme known for its dual-function capabilities in peroxygenase and peroxidase activities, we investigated the oxidative dimerization of 1-methoxynaphthalene. This biocatalysis involves multiple intermediates, including resonating radical forms. By transposing the enzyme reaction into a 500 mM ammonium acetate buffer and spraying it into a mass spectrometer, we could detect various transient intermediate species, suggesting their preservation in buffer droplets during their flight. The resonance-like radical intermediates were distinguished and temporally evaluated using a parallel reaction monitoring approach in tandem mass spectrometry after being trapped with TEMPO, a radical marker. This comprehensive analysis successfully elucidated the complete catalytic cycle of the enzyme, offering a robust method for gaining deeper insights into enzyme action by tracking multiple intermediates in real time.

Highly Stereoselective 1,2-cis-Xylosylation Enabled by Reagent Modulation, Remote Participation, and Electron-Withdrawing Synergistic Effects

Stereoselective constructions of 1,2-cis-glycosidic bonds are long-standing challenges in chemical synthesis. In particular, achieving highly stereoselective 1,2-cis-xylosylation remains a difficult task in carbohydrates chemistry. Here, we report that highly stereoselective 1,2-cis-xylosylation could be achieved via synergistic combinations of reagent modulation, remote participation, and electron-withdrawing effects. A variety of α-xylosides motifs have been effectively prepared by this 1,2-cis-xylosylation protocol, including hemicellulose xyloglucan, xyloglucosyl trisaccharide motif from mammalian cells, core M3 matriglycan motif, and even α-(1→3)-xylosides up to 12-mer. Furthermore, DFT calculations provided the origins of this stereoselective and synergistic 1,2-cis-xylosylation through SN1 and SN2 pathways.

Decoding Sugars: Mass Spectrometric Advances in the Analysis of the Sugar Alphabet

Monosaccharides play a central role in metabolic networks and in the biosynthesis of glycomolecules, which perform essential functions across all domains of life. Thus, identifying and quantifying these building blocks is crucial in both research and industry. Routine methods have been established to facilitate the analysis of common monosaccharides. However, despite the presence of common metabolites, most organisms utilize distinct sets of monosaccharides and derivatives. These molecules therefore display a large diversity, potentially numbering in the hundreds or thousands, with many still unknown. This complexity presents significant challenges in the study of glycomolecules, particularly in microbes, including pathogens and those with the potential to serve as novel model organisms. This review discusses mass spectrometric techniques for the isomer-sensitive analysis of monosaccharides, their derivatives, and activated forms. Although mass spectrometry allows for untargeted analysis and sensitive detection in complex matrices, the presence of stereoisomers and extensive modifications necessitates the integration of advanced chromatographic, electrophoretic, ion mobility, or ion spectroscopic methods. Furthermore, stable-isotope incorporation studies are critical in elucidating biosynthetic routes in novel organisms.

Mechanism of C-3 Acyl Neighboring Group Participation in Mannuronic Acid Glycosyl Donors

One of the main challenges in oligosaccharide synthesis is the stereoselective introduction of the glycosidic bond. In order to understand and control glycosylation reactions, thorough mechanistic studies are required. Reaction intermediates found by NMR spectroscopy often cannot explain the glycosylation's stereochemical outcome. Hence, reactions may proceed through low-abundance reaction intermediates that are difficult to detect, according to a Curtin-Hammett scenario. We have previously observed that manno-type sugars can engage in C-3 acyl neighboring group participation. Herein, we report the detection of glycosyl dioxanium ions that result from C-3 neighboring group participation in mannuronic acid donors. Using a suite of exchange NMR techniques, we were able to dissect the kinetics of the conformational ring-flip that precedes C-3 acyl participation and the participation event itself in various manno-type sugars. Hence, this study provides a complete picture of mannosyl dioxanium ion formation.

Stereoelectronic Effect of Protecting Groups on the Stability of Galactosyl Donor Intermediates

Using methods of DFT, we investigated the effect of electron withdrawing and electron donating groups on the relative stability of tentative glycosyl donor reaction intermediates. The calculation shows that by changing the stereoelectronic properties of the protecting group, we can influence the stability of the dioxolenium type of intermediates by up to 10 kcal mol-1, and that by increasing nucleophillicity of the 4-O-Bz group, the dioxolenium intermediate becomes more stable than a triflate-donor pair. We exploited this mechanism to design galactosyl donors with custom protecting groups on O2 and O4, and investigated the outcome of the reaction with cyclohexanol. The reaction showed no change in the product distribution, which suggests that the neighboring group participation takes precedence over remote group participation due to kinetic barriers.

Investigation of Neighboring Group Participation in 3,4-Diacetylated Glycosyl Donors in the Gas Phase

A key challenge in oligosaccharide synthesis is the stereoselective installation of glycosidic bonds. Each glycosidic linkage has one of two possible stereo-chemical geometries, α/β or 1,2-cis/trans. An established approach to install 1,2-trans glycosidic bonds is neighboring group participation (NGP), mediated by a 2-O-acyl group. Extension of this intramolecular stabilization to nucleophilic groups located at more remote positions has also been suggested, but remains poorly understood. Previously, we employed infrared ion spectroscopy to characterize the molecular ions of monoacetylated sugar donors and showed how the strength of the stabilizing effect depends on the position of the participating ester group on the glycosyl donor ring as well as on its relative stereochemistry. In this work, we investigated glycosyl donors carrying two acyl groups. Using isotope labelling and isomer population analysis we were able to resolving spectra of isomeric mixtures and establish the relative contribution of individual species. We conclude that 3,4-diacetyl mannosyl donors exclusively form a dioxanium ion as a result of C-3 acyl stabilization. In contrast, the glucosyl and galactosyl cations form mixtures of C-3 and C-4 acyl participation products. Hence, the combination of isotope labeling and population analysis allows for the study of increasingly complex glycosyl cations.

Mechanistic insight into benzylidene-directed glycosylation reactions using cryogenic infrared spectroscopy

The stereoselective formation of 1,2-cis glycosidic linkages is challenging. The currently most widely used strategy for their installation uses 4,6-O-benzylidene-protected building blocks. The stereoselectivity of this reaction is thought to be driven by a covalent intermediate, which reacts via an SN2 mechanism. However, the role of cationic SN1-type intermediates in this reaction is unclear. Here we elucidate the structure of glycosyl cations carrying 4,6-O-benzylidene groups using cryogenic infrared ion spectroscopy and computational methods. The data reveal that the intermediates form anhydro cations, which correlates well with the stereoselective outcome of SN1-type glycosylations. The study highlights how cryogenic infrared spectroscopy can elucidate the role of intermediates in sugar chemistry and how these structural data can be linked to reactions in solution.

A time averaged semiclassical approach to IR spectroscopy

We propose a new semiclassical approach to the calculation of molecular IR spectra. The method employs the time averaging technique of Kaledin and Miller upon symmetrization of the quantum dipole-dipole autocorrelation function. Spectra at high and low temperatures are investigated. In the first case, we are able to point out the possible presence of hot bands in the molecular absorption line shape. In the second case, we are able to reproduce accurate IR spectra as demonstrated by a calculation of the IR spectrum of the water molecule, which is within 4% of the exact intensity. Our time averaged IR spectra can be directly compared to time averaged semiclassical power spectra as shown in an application to the CO2 molecule, which points out the differences between IR and power spectra and demonstrates that our new approach can identify active IR transitions correctly. Overall, the method features excellent accuracy in calculating absorption intensities and provides estimates for the frequencies of vibrations in agreement with the corresponding power spectra. In perspective, this work opens up the possibility to interface the new method with the semiclassical techniques developed for power spectra, such as the divide-and-conquer one, to get accurate IR spectra of complex and high-dimensional molecular systems.

Characterization of elusive rhamnosyl dioxanium ions and their application in complex oligosaccharide synthesis

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.

Anomeric Triflates versus Dioxanium Ions: Different Product-Forming Intermediates from 3-Acyl Benzylidene Mannosyl and Glucosyl Donors

Minimal structural differences in the structure of glycosyl donors can have a tremendous impact on their reactivity and the stereochemical outcome of their glycosylation reactions. Here, we used a combination of systematic glycosylation reactions, the characterization of potential reactive intermediates, and in-depth computational studies to study the disparate behavior of glycosylation systems involving benzylidene glucosyl and mannosyl donors. While these systems have been studied extensively, no satisfactory explanations are available for the differences observed between the 3-O-benzyl/benzoyl mannose and glucose donor systems. The potential energy surfaces of the different reaction pathways available for these donors provide an explanation for the contrasting behavior of seemingly very similar systems. Evidence has been provided for the intermediacy of benzylidene mannosyl 1,3-dioxanium ions, while the formation of the analogous 1,3-glucosyl dioxanium ions is thwarted by a prohibitively strong flagpole interaction of the C-2-O-benzyl group with the C-5 proton in moving toward the transition state, in which the glucose ring adopts a B2,5-conformation. This study provides an explanation for the intermediacy of 1,3-dioxanium ions in the mannosyl system and an answer to why these do not form from analogous glucosyl donors.

Detection and Characterization of Rapidly Equilibrating Glycosylation Reaction Intermediates Using Exchange NMR

The stereoselective introduction of glycosidic bonds (glycosylation) is one of the main challenges in the chemical synthesis of carbohydrates. Glycosylation reaction mechanisms are difficult to control because, in many cases, the exact reactive species driving product formation cannot be detected and the product outcome cannot be explained by the primary reaction intermediate observed. In these cases, reactions are expected to take place via other low-abundance reaction intermediates that are in rapid equilibrium with the primary reaction intermediate via a Curtin-Hammett scenario. Despite this principle being well-known in organic synthesis, mechanistic studies investigating this model in glycosylation reactions are complicated by the challenge of detecting the extremely short-lived reactive species responsible for product formation. Herein, we report the utilization of the chemical equilibrium between low-abundance reaction intermediates and the stable, readily observed α-glycosyl triflate intermediate in order to infer the structure of the former species by employing exchange NMR. Using this technique, we enabled the detection of reaction intermediates such as β-glycosyl triflates and glycosyl dioxanium ions. This demonstrates the power of exchange NMR to unravel reaction mechanisms as we aim to build a catalog of kinetic parameters, allowing for the understanding and eventual prediction of glycosylation reactions.

Stereodirecting Effect of Esters at the 4-Position of Galacto- and Glucopyranosyl Donors: Effect of 4-C-Methylation on Side-Chain Conformation and Donor Reactivity, and Influence of Concentration and Stoichiometry on Distal Group Participation

When generated in a mass spectrometer bridged bicyclic 1,3-dioxenium ions derived from 4-O-acylgalactopyranosyl, donors can be observed by infrared spectroscopy at cryogenic temperatures, but they are not seen in the solution phase in contrast to the fused bicyclic 1,3-dioxalenium ions of neighboring group participation. The inclusion of a 4-C-methyl group into a 4-O-benzoyl galactopyranosyl donor enables nuclear magnetic resonance observation of the bicyclic ion arising from participation by the distal ester, with the methyl group influence attributed to ester ground state conformation destabilization. We show that a 4-C-methyl group also influences the side-chain conformation, enforcing a gauche,trans conformation in gluco and galactopyranosides. Competition experiments reveal that the 4-C-methyl group has only a minor influence on the rate of reaction of 4-O-benzoyl or 4-O-benzyl-galacto and glucopyranosyl donors and, consequently, that participation by the distal ester does not result in kinetic acceleration (anchimeric assistance). We demonstrate that the stereoselectivity of the 4-O-benzoyl-4-C-methyl galactopyranosyl donor depends on reaction concentration and additive (diphenyl sulfoxide) stoichiometry and hence that participation by the distal ester is a borderline phenomenon in competition with standard glycosylation mechanisms. An analysis of a recent paper affirming participation by a remote pivalate ester is presented with alternative explanations for the observed phenomena.

An In Silico Infrared Spectral Library of Molecular Ions for Metabolite Identification

Infrared ion spectroscopy (IRIS) continues to see increasing use as an analytical tool for small-molecule identification in conjunction with mass spectrometry (MS). The IR spectrum of an m/z selected population of ions constitutes a unique fingerprint that is specific to the molecular structure. However, direct translation of an IR spectrum to a molecular structure remains challenging, as reference libraries of IR spectra of molecular ions largely do not exist. Quantum-chemically computed spectra can reliably be used as reference, but the challenge of selecting the candidate structures remains. Here, we introduce an in silico library of vibrational spectra of common MS adducts of over 4500 compounds found in the human metabolome database. In total, the library currently contains more than 75,000 spectra computed at the DFT level that can be queried with an experimental IR spectrum. Moreover, we introduce a database of 189 experimental IRIS spectra, which is employed to validate the automated spectral matching routines. This demonstrates that 75% of the metabolites in the experimental data set are correctly identified, based solely on their exact m/z and IRIS spectrum. Additionally, we demonstrate an approach for specifically identifying substructures by performing a search without m/z constraints to find structural analogues. Such an unsupervised search paves the way toward the de novo identification of unknowns that are absent in spectral libraries. We apply the in silico spectral library to identify an unknown in a plasma sample as 3-hydroxyhexanoic acid, highlighting the potential of the method.

Competing C-4 and C-5-Acyl Stabilization of Uronic Acid Glycosyl Cations

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.

Stabilization of Glucosyl Dioxolenium Ions by "Dual Participation" of the 2,2-Dimethyl-2-(ortho-nitrophenyl)acetyl (DMNPA) Protection Group for 1,2-cis-Glucosylation

The stereoselective introduction of glycosidic bonds is of paramount importance to oligosaccharide synthesis. Among the various chemical strategies to steer stereoselectivity, participation by either neighboring or distal acyl groups is used particularly often. Recently, the use of the 2,2-dimethyl-2-(ortho-nitrophenyl)acetyl (DMNPA) protection group was shown to offer enhanced stereoselective steering compared to other acyl groups. Here, we investigate the origin of the stereoselectivity induced by the DMNPA group through systematic glycosylation reactions and infrared ion spectroscopy (IRIS) combined with techniques such as isotopic labeling of the anomeric center and isomer population analysis. Our study indicates that the origin of the DMNPA stereoselectivity does not lie in the direct participation of the nitro moiety but in the formation of a dioxolenium ion that is strongly stabilized by the nitro group.