Dissecting the Essential Role of Anomeric β-Triflates in Glycosylation Reactions

Exploring the Dual Functions of Distal Acyl Group Direction in Various Nucleophilic Environments

A universal glycosylation strategy could significantly simplify glycoside synthesis. One approach to achieving this goal is through acyl group direction for the corresponding 1,2-, 1,3-, 1,4-, or 1,6-trans glycosylation; however, this approach has been challenging for glycosidic bonds that require distal equatorial-acyl group direction. We developed an approach in weakly nucleophilic environments for selective 1,4-trans glycosylation directed by the equatorial-4-O-acyl group. Here, we explored this condition in other distal acyl groups and found that, besides 1,n-trans direction, acyl groups also mediated hydrogen bonding between acyl groups and alcohols. The latter showed a diverse effect and classified the acyl group direction into axial and equatorial categories. Corresponding glycosylation conditions were distinguished as guidance for acyl group direction from either category. Hence, acyl group direction may serve as a general glycosylation strategy.

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.

Synthesis of sialyl halides with various acyl protective groups

Glycosyl halides are historically one of the first glycosyl donors used in glycosylation reactions, and interest in glycosylation reactions involving this class of glycosyl donors is currently increasing. New methods for their activation have been proposed and effective syntheses of oligosaccharides with their participation have been developed. At the same time, the possibilities of using these approaches to the synthesis of sialosides are restricted by the limited diversity of known sialyl halides (previously, mainly sialyl chlorides, less often sialyl bromides and sialyl fluorides, with acetyl (Ac) groups at the oxygen atoms and AcNH, Ac2N and N3 groups at C-5 were used). This work describes the synthesis of six new N-acetyl- and N-trifluoroacetyl-sialyl chlorides and bromides with O-chloroacetyl and O-trifluoroacetyl protective groups. Preparation of N,O-trifluoroacetyl protected derivatives was made possible due to development of the synthesis of sialic acid methyl ester pentaol with N-trifluoroacetyl group.

On the influence of solvent on the stereoselectivity of glycosylation reactions

Methodology development in carbohydrate chemistry entails the stereoselective formation of C-O bonds as a key step in the synthesis of oligo- and polysaccharides. The anomeric selectivity of a glycosylation reaction is affected by a multitude of parameters, such as the nature of the donor and acceptor, activator/promotor system, temperature and solvent. The influence of different solvents on the stereoselective outcome of glycosylation reactions employing thioglucopyranosides as glycosyl donors with a non-participating protecting group at position 2 has been studied. A large change in selectivity as a function of solvent was observed and a correlation between selectivity and the Kamlet-Taft solvent parameter π* was found. Furthermore, molecular modeling using density functional theory methodology was conducted to decipher the role of the solvent and possible reaction pathways were investigated.

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.

Tf2O-Promoted Regioselective Heteronucleophilic Ring-Opening Approaches of Tetrahydrofuran

The ring-opening functionalization strategy in tetrahydrofuran (THF) represents an ideal approach to access different valuable structures. Herein, we report different operationally simple, efficient, unique, and practical regioselective heteronucleophilic ring-opening strategies for the THF system. Tf2O, which is a strong electrophilic activator, was found to generate a THF triflate intermediate that triggers the nucleophilicity of nitriles (Nu1) and led to regioselective ring opening in the presence of different nucleophiles (Nu2). Furthermore, the synthesis of different heteronucleophilic ring-opening dimerization products was attributed to the nucleophilicity of Nu2. We also demonstrated that use of borane-tetrahydrofuran (BTHF) can achieve challenging hydride addition in a similar manner.

Unraveling the promoter effect and the roles of counterion exchange in glycosylation reaction

The stereoselectivity of glycosidic bond formation continues to pose a noteworthy hurdle in synthesizing carbohydrates, primarily due to the simultaneous occurrence of SN1 and SN2 processes during the glycosylation reaction. Here, we applied an in-depth analysis of the glycosylation mechanism by using low-temperature nuclear magnetic resonance and statistical approaches. A pathway driven by counterion exchanges and reaction byproducts was first discovered to outline the stereocontributions of intermediates. Moreover, the relative reactivity values, acceptor nucleophilic constants, and Hammett substituent constants (σ values) provided a general index to indicate the mechanistic pathways. These results could allow building block tailoring and reaction condition optimization in carbohydrate synthesis to be greatly facilitated and simplified.

Substrate specific closed-loop optimization of carbohydrate protective group chemistry using Bayesian optimization and transfer learning

A new way of performing reaction optimization within carbohydrate chemistry is presented. This is done by performing closed-loop optimization of regioselective benzoylation of unprotected glycosides using Bayesian optimization. Both 6-O-monobenzoylations and 3,6-O-dibenzoylations of three different monosaccharides are optimized. A novel transfer learning approach, where data from previous optimizations of different substrates is used to speed up the optimizations, has also been developed. The optimal conditions found by the Bayesian optimization algorithm provide new insight into substrate specificity, as the conditions found are significantly different. In most cases, the optimal conditions include Et₃N and benzoic anhydride, a new reagent combination for these reactions, discovered by the algorithm, demonstrating the power of this concept to widen the chemical space. Further, the developed procedures include ambient conditions and short reaction times.

Stereoselective Synthesis of 2-Deoxy Glycosides via Iron Catalysis

An Fe-catalyzed 2-deoxy glycosylation method was developed from 3,4-O-carbonate glycals directly at room temperature. This novel approach enabled facile access to alkyl and aryl 2-deoxy glycosides in high yields with exclusive α-stereoselectivity, tolerating various alcohols, phenols, and glycals. The synthetic utility and advantage of this strategy have been demonstrated by the modification of six natural products and the construction of a tetrasaccharide.

Involvement of an Oxonium Ion Intermediate in Controlling the Diastereoselectivity of Nucleophilic Substitution Reactions of Septanoses

The alkoxy substituents at C4 and C2 of septanoses control the stereochemical outcomes of O-glycosylation reactions of these seven-membered-ring intermediates. Isolation of a bicyclic acetal byproduct in some substitution reactions suggests that the C4 benzyloxy substituent engaged in long-range participation, stabilizing intermediates by the formation of an oxonium ion intermediate. Inductive destabilization of the carbocationic intermediate provided by the C2 substituent is crucial to the participation of the remote alkoxy group.

Influence of Various Silyl Protecting Groups on Stereoselective 2-Deoxyrhamnosylation

The influence of various silyl protecting groups on 2-deoxyrhamnosylation using 2-deoxyrhamnosyl acetates, thioglycosides, and (p-methoxyphenyl)vinylbenzoate (PMPVB) donors has been presented. C-Glycosylation reactions reveal that tert-butyldimethylsilyl (TBDMS), triisopropylsilyl (TIPS), and tert-butyldiphenylsilyl (TBDPS) silyl protected rhamnosyl oxocarbenium ions have no facial selectivity except for the conformationally (⁴H₃) locked tetraisopropyldisiloxane (TIPDS) protected rhamnose donor, which provides complete α-selectivity. However, TBDPS protected rhamnosyl donors are found to be superior protecting groups for α-stereoselective O-glycosylation reactions with various acceptors. The observed results are found consistent across donors and donor activation conditions. Most importantly, the study was conducted at room temperature unlike the other energy-intensive low-temperature studies and was bound to have more practical utility. The outcomes have been explained using kinetic and thermodynamic analyses.

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.

The Influence of the Electron Density in Acyl Protecting Groups on the Selectivity of Galactose Formation

The stereoselective formation of 1,2-cis-glycosidic bonds is a major bottleneck in the synthesis of carbohydrates. We here investigate how the electron density in acyl protecting groups influences the stereoselectivity by fine-tuning the efficiency of remote participation. Electron-rich C4-pivaloylated galactose building blocks show an unprecedented α-selectivity. The trifluoroacetylated counterpart with electron-withdrawing groups, on the other hand, exhibits a lower selectivity. Cryogenic infrared spectroscopy in helium nanodroplets and density functional theory calculations revealed the existence of dioxolenium-type intermediates for this reaction, which suggests that remote participation of the pivaloyl protecting group is the origin of the high α-selectivity of the pivaloylated building blocks. According to these findings, an α-selective galactose building block for glycosynthesis is developed based on rational considerations and is subsequently employed in automated glycan assembly exhibiting complete stereoselectivity. Based on the obtained selectivities in the glycosylation reactions and the results from infrared spectroscopy and density functional theory, we suggest a mechanism by which these reactions could proceed.

C7 Epimerization of Benzylidene-Protected β-d-Idopyranosides Brings Structural Insights into Idose Conformational Flexibility

Idose is unique among other aldohexoses because of its high conformational flexibility in solution. We herein show that benzylidene acetal-protected 3-O-acyl-β-d-idopyranosides undergo Lewis acid-catalyzed C7 epimerization with concomitant ⁴C₁ to ¹C₄ ring inversion. The reaction conditions and structural parameters for this transformation to occur have been thoroughly investigated through an extensive glycosylation study combined with NMR analyses, X-ray diffraction, and quantum molecular modeling. In addition to reporting a direct, β-stereoselective idosylation approach, our work brings fundamental structural insights into the conformational flexibility of idose.

Nitro-Activated Nucleobase Exchange in the Synthesis of 2'-Fluoro-2'-Deoxyribonucleosides

Functionalized nucleosides bearing pyrimidine or purine bases can be prepared by activation of accessible pyrimidine nucleosides and subsequent transglycosylation. Nitration of lumicitabine, a 2'-fluoro-2'-deoxycytidine class antiviral agent, and its 2'-fluoro-2'-deoxyuridine precursor produce the same 5-nitro-2'-fluoro-2'-deoxyuridine. Under Vorbrüggen conditions, 5-nitrouracil serves as the leaving nucleobase and enables exchange with pyrimidine and purine nucleobases to anomeric 2'-fluoro-2'-deoxyribonucleosides in favor of β-anomers generally. The strategy is also applied in the isotopic labeling of 2'-fluoro-2'-deoxyuridines.

Recent Advances in Stereoselective Chemical O-Glycosylation Reactions

Carbohydrates involving glycoconjugates play a pivotal role in many life processes. Better understanding toward glycobiological events including the structure–function relationship of these biomolecules and for diagnostic and therapeutic purposes including tailor-made vaccine development and synthesis of structurally well-defined oligosaccharides (OS) become important. Efficient chemical glycosylation in high yield and stereoselectivity is however challenging and depends on the fine tuning of a protection profile to get matching glycosyl donor–acceptor reactivity along with proper use of other important external factors like catalyst, solvent, temperature, activator, and additive. So far, many glycosylation methods have been reported including several reviews also. In the present review, we will concentrate our discussion on the recent trend on α- and β-selective glycosylation reactions reported during the past decade.

More than a Leaving Group: N-Phenyltrifluoroacetimidate as a Remote Directing Group for Highly α-Selective 1,2-cis Glycosylation

The anomeric configuration can greatly affect the biological functions and activities of carbohydrates. Herein, we report that N-phenyltrifluoroacetimidoyl (PTFAI), a well-known leaving group for catalytic glycosylation, can act as a stereodirecting group for the challenging 1,2-cis α-glycosylation. Utilizing rapidly accessible 1,6-di-OPTFAI glycosyl donors, TMSOTf-catalyzed glycosylation occurred with excellent α-selectivity and broad substrate scope, and the remaining 6-OPTFAI group can be cleaved chemoselectively. The remote participation of 6-OPTFAI is supported by the first characterization of the crucial 1,6-bridged bicyclic oxazepinium ion intermediates by low-temperature NMR spectroscopy. These cations were found to be relatively stable and mainly responsible for the present stereoselectivities. Further application is highlighted in glycosylation reactions toward trisaccharide heparins as well as the convergent synthesis of chacotriose derivatives using a bulky 2,4-di-O-glycosylated donor.

Hyperconjugative Interactions of the Carbon-Halogen Bond that Influence the Geometry of Cyclic α-Haloacetals

The analysis of the structures of low-energy conformers of different α-haloacetals reveals changes in bond lengths and geometries that correspond to stabilizing orbital interactions that contribute to the ground-state structures of these systems. Several factors, including the electron-donating and electron-accepting abilities of the substituents on the ring, affect the degree of the electronic interactions in these carbohydrate-like systems. The presence of an α-halogen atom that can participate in hyperconjugation has been shown to contribute to the structural characteristics of the low-energy conformer. The experimental evidence is supported by natural bond order (NBO) analysis to identify the types of interactions and to assess their relative importance.

Anomeric Thioglycosides Give Different Anomeric Product Distributions under NIS/TfOH Activation

The reaction of a series of anomeric thioglycosides with various glycosyl acceptors and N-iodosuccinimide/catalytic triflic acid was investigated with respect to reactivity and anomeric selectivity. In general, β-configured donors were found to give a more β-selective reaction outcome compared to their α-configured counterparts. The relative reactivity of various thioglycosides was measured through competition experiments, and the following order was established: phenyl, tolyl, methyl, ethyl, isopropyl, and 1-adamantyl.

Computational discoveries of reaction mechanisms: recent highlights and emerging challenges

This review examines some of the notable advances and trends that have shaped the field of computational elucidation of organic reaction mechanisms over the last 10-15 years. It highlights the types of mechanistic problems that have recently become possible to study and summarizes the methodological developments that have permitted these new advances. Case studies are taken from three representative areas of organic chemistry-asymmetric catalysis, glycosylation reactions, and single electron transfer reactions-which illustrate themes common to the broader field. These include the trend towards modelling systems that are increasingly complex (both structurally and mechanistically), the growing appreciation of the mechanistic roles of non-covalent interactions, and the increasing ability to explore dynamical features of reaction mechanisms. Some interesting new challenges that have emerged in the field are identified.

Catalytic Stereoselective Synthesis of 2-Deoxy α-glycosides Using Glycosyl Ortho-[1-(p-MeOPhenyl)Vinyl]Benzoates (PMPVB) Donors

2-Deoxy Glycosyl Ortho-[1-(p-MeOPhenyl)Vinyl]Benzoates (PMPVB) donors have been presented as stable, reactive glycosyl donors for the synthesis of 2-deoxy α-glycosides. The donors react under Brønsted acid conditions to provide the 2-deoxy-α-glycosides...

Zinc(II) Iodide-Directed β-Mannosylation: Reaction Selectivity, Mode, and Application

A direct, efficient, and versatile glycosylation methodology promises the systematic synthesis of oligosaccharides and glycoconjugates in a streamlined fashion like the synthesis of medium to long-chain nucleotides and peptides. The development of a generally applicable approach for the construction of 1,2-cis-glycosidic bond with controlled stereoselectivity remains a major challenge, especially for the synthesis of β-mannosides. Here, we report a direct mannosylation strategy mediated by ZnI₂, a mild Lewis acid, for the highly stereoselective construction of 1,2-cis-β linkages employing easily accessible 4,6-O-tethered mannosyl trichloroacetimidate donors. The versatility and effectiveness of this strategy were demonstrated with successful β-mannosylation of a wide variety of alcohol acceptors, including complex natural products, amino acids, and glycosides. Through iteratively performing ZnI₂-mediated mannosylation with the chitobiosyl azide acceptor followed by site-selective deprotection of the mannosylation product, the novel methodology enables the modular synthesis of the key intermediate trisaccharide with Man-β-(1 → 4)-GlcNAc-β-(1 → 4)-GlcNAc linkage for N-glycan synthesis. Theoretical investigations with density functional theory calculations delved into the mechanistic details of this β-selective mannosylation and elucidated two zinc cations' essential roles as the activating agent of the donor and the principal mediator of the cis-directing intermolecular interaction.

A Stereoselective Glycosylation Approach to the Construction of 1,2-trans-β-d-Glycosidic Linkages and Convergent Synthesis of Saponins

Conventional syntheses of 1,2-trans-β-d- or α-l-glycosidic linkages rely mainly on neighboring group participation in the glycosylation reactions. The requirement for a neighboring participation group (NPG) excludes direct glycosylation with (1→2)-linked glycan donors, thus only allowing stepwise assembly of glycans and glycoconjugates containing this type of common motif. Here, a robust glycosylation protocol for the synthesis of 1,2-trans-β-d- or α-l-glycosidic linkages without resorting to NPG is disclosed; it employs an optimal combination of glycosyl N-phenyltrifluroacetimidates as donors, FeCl₃ as promoter, and CH₂ Cl₂ /nitrile as solvent. A broad substrate scope has been demonstrated by glycosylations with 12 (1→2)-linked di- and trisaccharide donors and 13 alcoholic acceptors including eight complex triterpene derivatives. Most of the glycosylation reactions are high yielding and exclusively 1,2-trans selective. Ten representative, naturally occurring triterpene saponins were thus synthesized in a convergent manner after deprotection of the coupled glycosides. Intensive mechanistic studies indicated that this glycosylation proceeds by S_N 2-type substitution of the glycosyl α-nitrilium intermediates. Importantly, FeCl₃ dissociates and coordinates with nitrile into [Fe(RCN)_n Cl₂ ]⁺ and [FeCl₄ ]^- , and the ferric cationic species coordinates with the alcoholic acceptor to provide a protic species that activates the imidate, meanwhile the poor nucleophilicity of [FeCl₄ ]^- ensures an uninterruptive role for the glycosidation.

Glycosyl Sulfonates Beyond Triflates

While glycosyl triflates are frequently invoked as intermediates in many chemical glycosylation reactions, the chemistry of other glycosyl sulfonates remains comparatively underexplored. Given the reactivity of sulfonates can span several orders of magnitude, this represents an untapped resource for the development of stereoselective glycosylation reactions. This personal account describes our laboratories efforts to take advantage of this reactivity to develop β-specific glycosylation reactions. Initial investigations led to the development of 2-deoxy-sugar tosylates as highly selective donors for β-glycoside synthesis, an approach which has been used to great success by our group and others for the construction of deoxy-sugar oligosaccharides and natural products. Subsequent studies demonstrate that "matching" the reactivity of the sulfonate to that of the sugar donor leads to highly selective SN 2-glycosylations with a range of substrates.

Guidelines for O-Glycoside Formation from First Principles

With a view to reducing the notorious complexity and irreproducibility of glycosylation reactions, 12 guidelines for the choice of concentration, temperature, and counterions are adumbrated.

Characterization of Mannosyl Dioxanium Ions in Solution Using Chemical Exchange Saturation Transfer NMR

The stereoselective introduction of the glycosidic bond remains one of the main challenges in carbohydrate synthesis. Characterizing the reactive intermediates of this reaction is key to develop stereoselective glycosylation reactions. Herein we report the characterization of low-populated, rapidly equilibrating, mannosyl dioxanium ions that arise from participation of a C-3 acyl group using chemical exchange saturation transfer (CEST) NMR spectroscopy. Dioxanium ion structure and equilibration kinetics were measured under relevant glycosylation conditions and highly α -selective couplings were observed suggesting glycosylation took place via this elusive intermediate.

Influence of Configuration at the 4- and 6-Positions on the Conformation and Anomeric Reactivity and Selectivity of 7-Deoxyheptopyranosyl Donors: Discovery of a Highly Equatorially Selective l-glycero-d-gluco-Heptopyranosyl Donor

The preparation of four per-O-benzyl-d- or l-glycero-d-galacto and d- or l-glycero-d-gluco heptopyranosyl sulfoxides and the influence of their side-chain conformations on reactivity and stereoselectivity in glycosylation reactions are described. The side-chain conformation in these donors is determined by the relative configuration of its point of attachment to the pyranoside ring and the two flanking centers in agreement with a recent model. In the d- and l-glycero-d-galacto glycosyl donors, the d-glycero-d-galacto isomer with the more electron-withdrawing trans,gauche conformation of its side chain was the more equatorially selective isomer. In the d- and l-glycero-d-gluco glycosyl donors, the l-glycero-d-gluco isomer with the least disarming gauche,gauche side-chain conformation was the most equatorially selective donor. Variable temperature NMR studies, while supporting the formation of intermediate glycosyl triflates at -80 °C in all cases, were inconclusive owing to a change in the decomposition mechanism with the change in configuration. It is suggested that the equatorial selectivity of the l-glycero-d-gluco isomer arises from H-bonding between the glycosyl acceptor and O6 of the donor, which is poised to deliver the acceptor antiperiplanar to the glycosyl triflate, resulting in a high degree of S_N2 character in the displacement reaction.

Aglycon reactivity as a guiding principle in latent-active approach to chemical glycosylations

Chemical glycosylations critically depend on the activation of a glycosyl donor and the reaction of this activated donor intermediate with an acceptor alcohol. Whereas many strategies are developed for the activation of an anomeric aglycon substituent, the latent-active method of glycosylation is based specifically on tuning the reactivity of the aglycon substituent of a glycosyl donor. Several novel methods have emerged to install reactive aglycon moiety in a glycosyl donor and fine-tuning the reactivity of the moiety. Remote functionalizations of the aglycon plays a key role in the reactivity tuning. Activation of a remote functionality enables an otherwise latent aglycon to an active moiety, suitable as a glycosyl donor. The latent-active approach provides an advantage to avoid the conversion of the aglycon to another donor prior to a glycosylation, in addition to advancing the contemporary glycosylations with alternate insights. The review analyzes the methodologies that consolidate the latent-active approach to chemical glycosylations.

Aromatic interactions in Glycochemistry: from molecular recognition to catalysis

Aromatic platforms are ubiquitous recognition motifs occurring in protein carbohydrate binding domains (CBDs), RNA receptors and enzymes. They stabilize the glycoside/receptor complexes by participating in stacking CH/π interactions with either the α- or β- face of the corresponding pyranose units. In addition, the role played by aromatic units in the stabilization of glycoside cationic transition states has started being recognized in recent years. Extensive studies carried out during the last decade have allowed to dissect the main contributing forces that stabilize the carbohydrate/aromatic complexes, while helping delineate not only the standing relationship between the glycoside/aromatic chemical structures and the strength of this interaction, but also their potential influence on glycoside reactivity.

Glycosyl Oxocarbenium Ions: Structure, Conformation, Reactivity, and Interactions

Carbohydrates (glycans, saccharides, and sugars) are essential molecules in all domains of life. Research on glycoscience spans from chemistry to biomedicine, including material science and biotechnology. Access to pure and well-defined complex glycans using synthetic methods depends on the success of the employed glycosylation reaction. In most cases, the mechanism of the glycosylation reaction is believed to involve the oxocarbenium ion. Understanding the structure, conformation, reactivity, and interactions of this glycosyl cation is essential to predict the outcome of the reaction. In this Account, building on our contributions on this topic, we discuss the theoretical and experimental approaches that have been employed to decipher the key features of glycosyl cations, from their structures to their interactions and reactivity.We also highlight that, from a chemical perspective, the glycosylation reaction can be described as a continuum, from unimolecular SN1 with naked oxocarbenium cations as intermediates to bimolecular SN2-type mechanisms, which involve the key role of counterions and donors. All these factors should be considered and are discussed herein. The importance of dissociative mechanisms (involving contact ion pairs, solvent-separated ion pairs, solvent-equilibrated ion pairs) with bimolecular features in most reactions is also highlighted.The role of theoretical calculations to predict the conformation, dynamics, and reactivity of the oxocarbenium ion is also discussed, highlighting the advances in this field that now allow access to the conformational preferences of a variety of oxocarbenium ions and their reactivities under SN1-like conditions.Specifically, the ground-breaking use of superacids to generate these cations is emphasized, since it has permitted characterization of the structure and conformation of a variety of glycosyl oxocarbenium ions in superacid solution by NMR spectroscopy.We also pay special attention to the reactivity of these glycosyl ions, which depends on the conditions, including the counterions, the possible intra- or intermolecular participation of functional groups that may stabilize the cation and the chemical nature of the acceptor, either weak or strong nucleophile. We discuss recent investigations from different experimental perspectives, which identified the involved ionic intermediates, estimating their lifetimes and reactivities and studying their interactions with other molecules. In this context, we also emphasize the relationship between the chemical methods that can be employed to modulate the sensitivity of glycosyl cations and the way in which glycosyl modifying enzymes (glycosyl hydrolases and transferases) build and cleave glycosidic linkages in nature. This comparison provides inspiration on the use of molecules that regulate the stability and reactivity of glycosyl cations.

Automated Quantification of Hydroxyl Reactivities: Prediction of Glycosylation Reactions

The stereoselectivity and yield in glycosylation reactions are paramount but unpredictable. We have developed a database of acceptor nucleophilic constants (Aka) to quantify the nucleophilicity of hydroxyl groups in glycosylation influenced by the steric, electronic and structural effects, providing a connection between experiments and computer algorithms. The subtle reactivity differences among the hydroxyl groups on various carbohydrate molecules can be defined by Aka, which is easily accessible by a simple and convenient automation system to assure high reproducibility and accuracy. A diverse range of glycosylation donors and acceptors with well-defined reactivity and promoters were organized and processed by the designed software program "GlycoComputer" for prediction of glycosylation reactions without involving sophisticated computational processing. The importance of Aka was further verified by random forest algorithm, and the applicability was tested by the synthesis of a Lewis A skeleton to show that the stereoselectivity and yield can be accurately estimated.

Computational evidence of glycosyl cations

Glycosyl cations are key intermediates in the glycosylation reactions taking place through a S_N1-type mechanism. To obtain a reliable description of the glycosylation reaction mechanism a combination of computational studies and experimental data such as kinetic isotopic effects is needed. Computational studies have elucidated S_N2-type glycosylation reaction mechanisms, but elucidation of mechanisms in which ion pairs can be formed presents some difficulties because of the recombination of the ions. Recent topological and dynamic studies open the door to the ultimate confirmation of the presence of glycosyl cations in the form of intimate ion pairs during certain glycosylation reactions. This review covers the state-of-the-art tools and applications of computational chemistry mainly developed during the last ten years to understand glycosylation reactions in which an oxocarbenium ion could be involved.

Ab Initio Molecular Dynamics Simulations of the SN1/SN2 Mechanistic Continuum in Glycosylation Reactions

We report a computational approach to evaluate the reaction mechanisms of glycosylation using ab initio molecular dynamics (AIMD) simulations in explicit solvent. The reaction pathways are simulated via free energy calculations based on metadynamics and trajectory simulations using Born-Oppenheimer molecular dynamics. We applied this approach to investigate the mechanisms of the glycosylation of glucosyl α-trichloroacetimidate with three acceptors (EtOH, i-PrOH, and t-BuOH) in three solvents (ACN, DCM, and MTBE). The reactants and the solvents are treated explicitly using density functional theory. We show that the profile of the free energy surface, the synchronicity of the transition state structure, and the time gap between leaving group dissociation and nucleophile association can be used as three complementary indicators to describe the glycosylation mechanism within the SN1/SN2 continuum for a given reaction. This approach provides a reliable means to rationalize and predict reaction mechanisms and to estimate lifetimes of oxocarbenium intermediates and their dependence on the glycosyl donor, acceptor, and solvent environment.

En Route to the Transformation of Glycoscience: A Chemist's Perspective on Internal and External Crossroads in Glycochemistry

Carbohydrate chemistry is an essential component of the glycosciences and is fundamental to their progress. This Perspective takes the position that carbohydrate chemistry, or glycochemistry, has reached three crossroads on the path to the transformation of the glycosciences, and illustrates them with examples from the author's and other laboratories. The first of these potential inflexion points concerns the mechanism of the glycosylation reaction and the role of protecting groups. It is argued that the experimental evidence supports bimolecular SN2-like mechanisms for typical glycosylation reactions over unimolecular ones involving stereoselective attack on naked glycosyl oxocarbenium ions. Similarly, it is argued that the experimental evidence does not support long-range stereodirecting participation of remote esters through bridged bicyclic dioxacarbenium ions in organic solution in the presence of typical counterions. Rational design and improvement of glycosylation reactions must take into account the roles of the counterion and of concentration. A second crossroads is that between mainstream organic chemistry and glycan synthesis. The case is made that the only real difference between glycan and organic synthesis is the formation of C-O rather than C-C bonds, with diastereocontrol, strategy, tactics, and elegance being of critical importance in both areas: mainstream organic chemists should feel comfortable taking this fork in the road, just as carbohydrate chemists should traveling in the opposite direction. A third crossroads is that between carbohydrate chemistry and medicinal chemistry, where there are equally many opportunities for traffic in either direction. The glycosciences have advanced enormously in the past decade or so, but creativity, input, and ingenuity of scientists from all fields is needed to address the many sophisticated challenges that remain, not the least of which is the development of a broader and more general array of stereospecific glycosylation reactions.

Statistical Analysis of Glycosylation Reactions

Chemical synthesis is one of the practical approaches to access carbohydrate-based natural products and their derivatives with high quality and in a large quantity. However, stereoselectivity during the glycosylation reaction is the main challenge because the reaction can generate both α- and β-glycosides. The main focus of the present article is the concept of recent mechanistic studies that have applied statistical analysis and quantitation for defining stereoselective changes during the reaction process. Based on experimental evidence, a detailed discussion associated with the mechanism and degree of influence affecting the stereoselective outcome of glycosylation is included.