Plausible transition states for glycosylation reactions

Role of ion pairs in model glycosylation reactions of permethylated glucosyl and xylosyl triflates

Elucidating the molecular mechanisms of chemical O-glycosylation remains a significant challenge in glycochemistry. This study examines the mechanism of the nucleophilic substitution reaction between glycosyl triflates, which are extensively used in studies of glycosylation mechanisms, and several acceptor alcohols. The investigation was conducted through a comparative analysis of permethylated glucosyl triflate GTf and its xylosyl counterpart XTf. The glycosylation reactions, conducted in dichloromethane using GTf and XTf with EtOH, tBuOH, and CF3CH2OH, exhibited diverse α/β selectivities depending on the types of donor and acceptor molecules used. Identifying a unified mechanism to explain this range of selectivities proved challenging. Notably, we observed a distinct trend wherein the addition of excess triflate salt (Bu4NOTf) had a more pronounced effect on the α/β selectivity in glycosylation reactions utilizing XTf compared to those using GTf. Quantum chemical calculations performed at the SCS-MP2//DFT(M06-2X) level, with explicit inclusion of five solvent molecules, showed that contact ion pairs arising from XTf were significantly more stable than those from GTf. These experimental and computational results strongly suggest that ion pairs play a more crucial role in the glycosylation process involving XTf than GTf. Additionally, our quantum chemical analyses clarified that the enhanced stability of the ion pairs from XTf was attributed not to the strength of the C-1-OTf bond within XTf but to the flexibility in the conformational changes of XTf's pyranosyl ring.

Synthesis and Glycosidation of Anomeric Halides: Evolution from Early Studies to Modern Methods of the 21st Century

Advances in synthetic carbohydrate chemistry have dramatically improved access to common glycans. However, many novel methods still fail to adequately address challenges associated with chemical glycosylation and glycan synthesis. Since a challenge of glycosylation has remained, scientists have been frequently returning to the traditional glycosyl donors. This review is dedicated to glycosyl halides that have played crucial roles in shaping the field of glycosciences and continue to pave the way toward our understanding of chemical glycosylation.

Multifaceted Computational Modeling in Glycoscience

Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.

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.

Exploiting non-covalent interactions in selective carbohydrate synthesis

Non-covalent interactions (NCIs) are a vital component of biological bond-forming events, and have found important applications in multiple branches of chemistry. In recent years, the biomimetic exploitation of NCIs in challenging glycosidic bond formation and glycofunctionalizations has attracted significant interest across diverse communities of organic and carbohydrate chemists. This emerging theme is a major new direction in contemporary carbohydrate chemistry, and is rapidly gaining traction as a robust strategy to tackle long-standing issues such as anomeric and site selectivity. This Review thus seeks to provide a bird's-eye view of wide-ranging advances in harnessing NCIs within the broad field of synthetic carbohydrate chemistry. These include the exploitation of NCIs in non-covalent catalysed glycosylations, in non-covalent catalysed glycofunctionalizations, in aglycone delivery, in stabilization of intermediates and transition states, in the existence of intramolecular hydrogen bonding networks and in aggregation by hydrogen bonds. In addition, recent emerging opportunities in exploiting halogen bonding and other unconventional NCIs, such as CH-π, cation-π and cation-n interactions, in various aspects of carbohydrate chemistry are also examined.

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.

Automated Chemical Oligosaccharide Synthesis: Novel Approach to Traditional Challenges

Advances in carbohydrate chemistry have certainly made common oligosaccharides much more accessible. However, many current methods still rely heavily upon specialized knowledge of carbohydrate chemistry. The application of automated technologies to chemical and life science applications such as genomics and proteomics represents a vibrant field. These automated technologies also present opportunities for their application to organic synthesis, including that of the synthesis of oligosaccharides. However, application of automated methods to the synthesis of carbohydrates is an underdeveloped area as compared to other classes of biomolecules. The overarching goal of this review article is to present the advances that have been made at the interface of carbohydrate chemistry and automated technology.

The Experimental Evidence in Support of Glycosylation Mechanisms at the SN1-SN2 Interface

A critical review of the state-of-the-art evidence in support of the mechanisms of glycosylation reactions is provided. Factors affecting the stability of putative oxocarbenium ions as intermediates at the SN1 end of the mechanistic continuum are first surveyed before the evidence, spectroscopic and indirect, for the existence of such species on the time scale of glycosylation reactions is presented. Current models for diastereoselectivity in nucleophilic attack on oxocarbenium ions are then described. Evidence in support of the intermediacy of activated covalent glycosyl donors is reviewed, before the influences of the structure of the nucleophile, of the solvent, of temperature, and of donor-acceptor hydrogen bonding on the mechanism of glycosylation reactions are surveyed. Studies on the kinetics of glycosylation reactions and the use of kinetic isotope effects for the determination of transition-state structure are presented, before computational models are finally surveyed. The review concludes with a critical appraisal of the state of the art.

Immobilization of glycans on solid surfaces for application in glycomics

Carbohydrates are an important class of biomolecules which are involved in a multitude of cellular functions. In the field of glycomics, the structure and function of various carbohydrates, oligosaccharides, glycans and their conjugates are constantly under investigation. In the continuing quest to understand the roles of carbohydrates in their interactions with proteins, immunogens, and other cell-surface carbohydrates, scientists have developed methods for observing the effects of specific saccharide sequences on various cellular components. Carbohydrate immobilization has allowed researchers to study the impact of specific sequences, leading to a deeper understanding of many cellular processes. The goal of this review is to highlight the chemical reactions and interactions that have been used for glycan immobilization.

Bimodal concentration-dependent reactivity pattern of a glycosyl donor: Is the solution structure involved?

Changes in concentration (0.001-0.1 M) of an arabinofuranosyl donor (1) have been shown to modulate the temperature T at which activation of 1 occurs (from -23 °C to +7 °C), the reaction time (from 1.5 h to 3 days) and the yield of the disaccharide formed (from 14% to 82%). At concentrations exceeding 0.01 M, these parameters, as well as the specific optical rotation of the solution of 1, virtually do not depend on concentration suggesting formation of reacting species (supramers) of glycosyl donor with similar structures, hence reactivities, but considerably different from those formed in more dilute solutions. The found critical concentration (0.01 M) separates two concentration ranges of reaction solutions corresponding to two types of solution structure that are featured by the presence of fundamentally different supramers of glycosyl donor, which have distinct chemical properties. These results allow a fresh look at the problems of reactivity of chemical compounds and selectivity of the reactions in which they participate.

Mechanism of Glycosylation of Anomeric Sulfonium Ions

Anomeric sulfonium ions are attractive glycosyl donors for the stereoselective installation of 1,2-cis glycosides. Although these donors are receiving increasing attention, their mechanism of glycosylation remains controversial. We have investigated the reaction mechanism of glycosylation of a donor modified at C-2 with a (1S)-phenyl-2-(phenylsulfanyl)ethyl chiral auxiliary. Preactivation of this donor results in the formation of a bicyclic β-sulfonium ion that after addition of an alcohol undergoes 1,2-cis-glycosylation. To probe the importance of the thiophenyl moiety, analogs were prepared in which this moiety was replaced by an anisoyl or benzyl moiety. Furthermore, the auxiliaries were installed as S- and R-stereoisomers. It was found that the nature of the heteroatom and chirality of the auxiliary greatly influenced the anomeric outcome and only the one containing a thiophenyl moiety and having S-configuration gave consistently α-anomeric products. The sulfonium ions are sufficiently stable at a temperature at which glycosylations proceed indicating that they are viable glycosylation agents. Time-course NMR experiments with the latter donor showed that the initial rates of glycosylations increase with increases in acceptor concentration and the rate curves could be fitted to a second order rate equation. Collectively, these observations support a mechanism by which a sulfonium ion intermediate is formed as a trans-decalin ring system that can undergo glycosylation through a bimolecular mechanism. DFT calculations have provided further insight into the reaction path of glycosylation and indicate that initially a hydrogen-bonded complex is formed between sulfonium ion and acceptor that undergoes SN2-like glycosylation to give an α-anomeric product.

Cation Clock Reactions for the Determination of Relative Reaction Kinetics in Glycosylation Reactions: Applications to Gluco- and Mannopyranosyl Sulfoxide and Trichloroacetimidate Type Donors

The development of a cation clock method based on the intramolecular Sakurai reaction for probing the concentration dependence of the nucleophile in glycosylation reactions is described. The method is developed for the sulfoxide and trichloroacetimidate glycosylation protocols. The method reveals that O-glycosylation reactions have stronger concentration dependencies than C-glycosylation reactions consistent with a more associative, S(N)2-like character. For the 4,6-O-benzylidene-directed mannosylation reaction a significant difference in concentration dependence is found for the formation of the β- and α-anomers, suggesting a difference in mechanism and a rationale for the optimization of selectivity regardless of the type of donor employed. In the mannose series the cyclization reaction employed as clock results in the formation of cis and trans-fused oxabicyclo[4,4,0]decanes as products with the latter being strongly indicative of the involvement of a conformationally mobile transient glycosyl oxocarbenium ion. With identical protecting group arrays cyclization in the glucopyranose series is more rapid than in the mannopyranose manifold. The potential application of related clock reactions in other carbenium ion-based branches of organic synthesis is considered.

Carbohydrate-protein interactions: molecular modeling insights

The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.

A propos of glycosyl cations and the mechanism of chemical glycosylation; the current state of the art

An overview of recent advances in glycosylation with particular emphasis on mechanism is presented. The mounting evidence for both the existence of glycosyl oxocarbenium ions as fleeting intermediates in some reactions, and the crucial role of the associated counterion in others is discussed. The extremes of the SN1 and SN2 manifolds for the glycosylation reaction are bridged by a continuum of mechanisms in which it appears likely that most examples are located.

Hydrogen bond mediated aglycone delivery: synthesis of linear and branched α-glucans

A Hydrogen bond mediated aglycone delivery (HAD) method was applied to the synthesis of α-glucans, which are abundant in nature, but as targets represent a notable challenge to chemists. The synthesis of linear oligosaccharide sequences was accomplished in complete stereoselectivity in all glycosylations. The efficacy of HAD may diminish with the increased bulk of the glycosyl acceptor, and may be an important factor for the syntheses of oligomers beyond pentasaccharides. The synthesis of a branched structure proved more challenging, particularly with bulky trisaccharide acceptors.

In a glycosylation reaction how does a hydroxylic nucleophile find the activated anomeric carbon?

The mechanism by which nucleophilic hydroxyls are attracted to activated glycopyranosyl donors is not known. Besides the intrinsic attraction of oxygen centred negative dipoles towards the developing electron deficiency at the anomeric carbon only a few suggestions have been given in the literature. By studying the effect on Density Functional Theory (DFT) modelled glycosylation reactions on the presence of polar additives as tested with acetonitrile two possible effects have been identified. One was noted in a previous publication (Carbohydr. Res.2012, 356, 180-190) and two further examples discovered here that suggest that a lone pair of a nucleophile approaching a donor with a β-leaving group from the α-face can act as the antiperiplanar lone pair that assists leaving group departure. This interaction starts at just under a nucleophile C-1 separation of 3Å and has an incipient bond angle of O-5-C-1-Nuc(O or N) of very close to 90° which can be at C-1 with the p-type orbital at C-1-O-5 of the incipient oxacarbenium ion, that is, the LUMO of the activated donor. The 2nd interaction is less well studied and is suggested to be a similar bonding interaction which moves β-face nucleophiles to O-Nuc-C-1-leaving groups angles close to 180°.

Design of chemical glycosyl donors: does changing ring conformation influence selectivity/reactivity?

This tutorial review focuses on the design of glycosyl donors, especially on attempts to control selectivity/reactivity by employing bulky substituents, cyclic protecting groups, or bridged structures. These structural modifications are performed to change the conformational distributions of pyranoside/furanoside rings. We also briefly discuss this issue with regard to studies on furanosides and enzymatic glycosylation reactions. Readers will find that some of the designed glycosyl donors have been used to achieve total syntheses of natural products.

Stereoselective C-glycoside formation with 2-O-benzyl-4,6-O-benzylidene protected 3-deoxy gluco- and mannopyranoside donors: comparison with O-glycoside formation

Unlike alcohols, the reaction of C-nucleophiles with 2-O-benzyl-4,6-O-benzylidene-protected 3-deoxy-gluco- and mannopyranosyl thioglycosides is highly stereoselective providing the α-C-glycosides in the gluco-series and the β-C-glycosides in the manno-series. Conformational analysis of nucleophilic attack of putative intermediate glycosyl oxocarbenium ions suggests that the observed selectivities for C-glycoside formation can be explained by preferential attack on the opposite face of the oxocarbenium to the C2-H2 bond and that eclipsing interactions with this bond are the main stereodetermining factor. It is argued that the steric interactions in the attack of alcohols (sp(3)-hybridized O) and of typical carbon-based nucleophiles (sp(2) C) on oxocarbenium ions are very different, with the former being less severe, and thus that there is no a priori reason to expect O- and C-glycosylation to exhibit parallel stereoselectivities for attack on a given oxocarbenium ion.