Halogen, Chalcogen, Pnictogen, and Tetrel Bonding in Non-Covalent Organocatalysis: An Update

The use of noncovalent interactions based on electrophilic halogen, chalcogen, pnictogen, or tetrel centers in organocatalysis has gained noticeable attention. Herein, we provide an overview on the most important developments in the last years with a clear focus on experimental studies and on catalysts which act via such non-transient interactions.

Stereoselective Entry into α,α'-C-Oxepane Scaffolds through a Chalcogen Bonding Catalyzed Strain-Release C-Septanosylation Strategy

The utility of unconventional noncovalent interactions (NCIs) such as chalcogen bonding has lately emerged as a robust platform to access synthetically difficult glycosides stereoselectively. Herein, we disclose the versatility of a phosphonochalcogenide (PCH) catalyst to facilitate access into the challenging, but biologically interesting 7-membered ring α,α'-C-disubstituted oxepane core through an α-selective strain-release C-glycosylation. Methodically, this strategy represents a switch from more common but entropically less desired macrocyclizations to a thermodynamically favored ring-expansion approach. In light of the general lack of stereoselective methods to access C-septanosides, a remarkable palette of silyl-based nucleophiles can be reliably employed in our method. This include a broad variety of useful synthons, such as easily available silyl-allyl, silyl-enol ether, silyl-ketene acetal, vinylogous silyl-ketene acetal, silyl-alkyne and silylazide reagents. Mechanistic investigations suggest that a mechanistic shift towards an intramolecular aglycone transposition involving a pentacoordinate silicon intermediate is likely responsible in steering the stereoselectivity.

Harnessing Multistep Chalcogen Bonding Activation in the α-Stereoselective Synthesis of Iminoglycosides

The use of noncovalent interactions (NCIs) has received significant attention as a pivotal synthetic handle. Recently, the exploitation of unconventional NCIs has gained considerable traction in challenging reaction manifolds such as glycosylation due to their capacity to facilitate entry into difficult-to-access sugars and glycomimetics. While investigations involving oxacyclic pyrano- or furanoside scaffolds are relatively common, methods that allow the selective synthesis of biologically important iminosugars are comparatively rare. Here, we report the capacity of a phosphonochalcogenide (PCH) to catalyze the stereoselective α-iminoglycosylation of iminoglycals with a wide array of glycosyl acceptors with remarkable protecting group tolerance. Mechanistic studies have illuminated the counterintuitive role of the catalyst in serially activating both the glycosyl donor and acceptor in the up/downstream stages of the reaction through chalcogen bonding (ChB). The dynamic interaction of chalcogens with substrates opens up new mechanistic opportunities based on iterative ChB catalyst engagement and disengagement in multiple elementary steps.

Anion-Bridged Dual Hydrogen Bond Enabled Concerted Addition of Phenol to Glycal

A noncovalent organocatalytic concerted addition of phenol to glycal is developed for the stereoselective and regioselective construction of biologically important phenolic 2-deoxyglycosides, featuring wide substrate tolerance. The method relies on an anion-bridged dual hydrogen bond interaction which is experimentally proved by Nuclear Magnetic Resonance (NMR), Ultraviolet and visible (UV-vis), and fluorescence analysis. Experimental evidence including kinetic analysis, Kinetic Isotope Effect (KIE) studies, linear free energy relationship, Hammett plot, and density functional theory (DFT) calculations is provided for a concerted mechanism where a high-energy oxocarbenium ion is not formed. In addition, the potential utility of this method is further demonstrated by the synthesis of biologically active glycosylated flavones. The benchmarking studies demonstrate significant advances in this newly developed method compared to previous approaches.

Boronic Acid-Catalyzed Regio- and Stereoselective N-Glycosylations of Purines and Other Azole Heterocycles: Access to Nucleoside Analogues

In the presence of an arylboronic acid catalyst, azole-type heterocycles, including purines, tetrazoles, triazoles, indazoles, and benzo-fused congeners, undergo regio- and stereoselective N-glycosylations with furanosyl and pyranosyl trichloroacetimidate donors. The protocol, which does not require stoichiometric activators, specialized leaving groups, or drying agents, provides access to nucleoside analogues and enables late-stage N-glycosylation of azole-containing pharmaceutical agents. A mechanism involving simultaneous activation of the glycosyl donor and acceptor by the organoboron catalyst has been proposed, supported by kinetic analysis and computational modeling.

Exploiting π and Chalcogen Interactions for the β-Selective Glycosylation of Indoles through Glycal Conformational Distortion

Harnessing unconventional noncovalent interactions (NCIs) is emerging as a formidable synthetic approach in difficult-to-access glycosidic chemical space. C-Glycosylation, in particular, has gained a flurry of recent attention. However, most reported methods are restricted to the relatively facile access to α-C-glycosides. Herein, we disclose a β-stereoselective glycosylation of indoles by employing a phosphonoselenide catalyst. The robustness of this protocol is exemplified by its amenability for reaction at both the indolyl C- and N- reactivity sites. In contrast to previous reports, in which the chalcogens were solely involved in Lewis acidic activation, our mechanistic investigation unraveled that the often neglected flanking aromatic substituents of phosphonoselenides can substantially contribute to catalysis by engaging in π-interactions. Computations and NMR spectroscopy indicated that the chalcogenic and aromatic components of the catalyst can be collectively exploited to foster conformational distortion of the glycal away from the usual half-chair to the boat conformation, which liberates the convex β-face for nucleophilic attack.

Halogen Bond Catalysis: A Physical Chemistry Perspective

As important noncovalent interactions, halogen bonds have been widely used in material science, supramolecular chemistry, medicinal chemistry, organocatalysis, and other fields. In the past 15 years, halogen bond catalysis has become a developed field in organocatalysis for the catalysts' advantages of being environmentally friendly, inexpensive, and recyclable. Halogen bonds can induce various organic reactions, and halogen bond catalysis has become a powerful alternative to the fully explored hydrogen bond catalysis. From a physical chemistry view, this perspective provides an overview of the latest progress and key examples of halogen bond catalysis via activation of the lone pair systems of organic functional group, π systems, and metal complexes. The research progresses in halogen bond catalysis by our group were also introduced.

α/β-Stereo- and diastereoselective glycosylation with n-pentenyl glycoside donors, promoted by N-iodosuccinimide and catalyzed by chiral Brønsted acid

A method involving stereoselective glycosylation catalyzed by (+)-isomenthol ester of pentacarbomethoxycyclopentadiene as a chiral Brønsted acid, with n-pentenyl glycosides in the presence of N-iodosuccinimide as the promoter is described; this method offered a chiral recognition of racemic substrates.

Cooperative Bifurcated Chalcogen Bonding and Hydrogen Bonding as Stereocontrolling Elements for Selective Strain-Release Septanosylation

The exploitation of noncovalent interactions (NCIs) is emerging as a vital handle in tackling broad stereoselectivity challenges in synthesis. In particular, there has been significant recent interest in the harnessing of unconventional NCIs to surmount difficult selectivity challenges in glycosylations. Herein, we disclose the exploitation of an unconventional bifurcated chalcogen bonding and hydrogen bonding (HB) network, which paves the way for a robust catalytic strategy into biologically useful seven-membered ring sugars. Through 13C nuclear magnetic resonance (NMR) in situ monitoring, NMR titration experiments, and density functional theory (DFT) modeling, we propose a remarkable contemporaneous activation of multiple functional groups consisting of a bifurcated chalcogen bonding mechanism working hand-in-hand with HB activation. Significantly, the ester moiety installed on the glycosyl donor is critical in the establishment of the postulated ternary complex for stereocontrol. Through the 13C kinetic isotopic effect and kinetic studies, our data corroborated that a dissociative SNi-type mechanism forms the stereocontrolling basis for the excellent α-selectivity.

Palladium catalysis enables cross-coupling-like SN2-glycosylation of phenols

Despite their importance in life and material sciences, the efficient construction of stereo-defined glycosides remains a challenge. Studies of carbohydrate functions would be advanced if glycosylation methods were as reliable and modular as palladium (Pd)-catalyzed cross-coupling. However, Pd-catalysis excels in forming sp2-hybridized carbon centers whereas glycosylation mostly builds sp3-hybridized C-O linkages. We report a glycosylation platform through Pd-catalyzed SN2 displacement from phenols toward bench-stable, aryl-iodide-containing glycosyl sulfides. The key Pd(II) oxidative addition intermediate diverges from an arylating agent (Csp2 electrophile) to a glycosylating agent (Csp3 electrophile). This method inherits many merits of cross-coupling reactions, including operational simplicity and functional group tolerance. It preserves the SN2 mechanism for various substrates and is amenable to late-stage glycosylation of commercial drugs and natural products.

Balancing Activity and Stability in Halogen-Bonding Catalysis: Iodopyridinium-Catalyzed One-Pot Synthesis of 2,3-Dihydropyridinones

A one-pot cascade reaction for 2,3-dihydropyridinone synthesis was accomplished with 3-fluoro-2-iodo-1-methylpyridinium triflate as the halogen bond catalyst. The desired [4+2] cycloaddition products, bearing aryl, heteroaryl, alkyl, and alicyclic substituents, were successfully furnished in 28-99% yields. Mechanistic investigations proved that a strong halogen-bonding interaction forged between the iodopyridinium catalyst and imine intermediate was essential to dynamically masking the vulnerable C-I bond on the catalyst and accelerating the following aza-Diels-Alder reaction.

Synthesis of N-Glycosides by Silver-Assisted Gold Catalysis

The synthesis of N-glycosides from stable glycosyl donors in a catalytic fashion is still challenging, though they exist ubiquitously in DNA, RNA, glycoproteins, and other biological molecules. Herein, silver-assisted gold-catalyzed activation of alkynyl glycosyl carbonate donors is shown to be a versatile approach for the synthesis of purine and pyrimidine nucleosides, asparagine glycosides and quinolin-2-one N-glycosides. Thus synthesized nucleosides were subjected to the oxidation-reduction sequence for the conversion of Ribf- into Araf- nucleosides, giving access to nucleosides that are otherwise difficult to synthesize. Furthermore, the protocol is demonstrated to be suitable for the synthesis of 2'-modified nucleosides in a facile manner. Direct attachment of an asparagine-containing dipeptide to the glucopyranose and subsequent extrapolation to afford the dipeptide disaccharide unit of chloroviruses is yet another facet of this endeavor.

Chiral Bromonium Salt (Hypervalent Bromine(III)) with N-Nitrosamine as a Halogen-Bonding Bifunctional Catalyst

There has been a great focus on halogen-bonding as a unique interaction between electron-deficient halogen atoms with Lewis basic moieties. Although the application of halogen-bonded atoms in organic chemistry has been eagerly researched in these decades, the development of chiral molecules with halogen-bonding functionalities and their utilization in asymmetric catalysis are still in the\ir infancy. We have previously developed chiral halonium salts with amide functionalities, which behaved as excellent catalysts albeit in only two reactions due to the lack of substrate activation abilities. In this manuscript, we have developed chiral halonium salts with an N-nitrosamine moiety and applied them to the Mannich reaction of isatin-derived ketimines with malonic esters. The study focused on our novel bromonium salt catalyst which provided the corresponding products in high yields with up to 80% ee. DFT calculations of the chiral catalyst structure suggested that the high asymmetric induction abilities of this catalyst are due to the Lewis basic role of the N-nitrosamine part. To the best of our knowledge, this is the first catalytic application of N-nitrosamines.

Hydrogen bond activated glycosylation under mild conditions

Herein, we report a new glycosylation system for the highly efficient and stereoselective formation of glycosidic bonds using glycosyl N-phenyl trifluoroacetimidate (PTFAI) donors and a charged thiourea hydrogen-bond-donor catalyst. The glycosylation protocol features broad substrate scope, controllable stereoselectivity, good to excellent yields and exceptionally mild catalysis conditions. Benefitting from the mild reaction conditions, this new hydrogen bond-mediated glycosylation system in combination with a hydrogen bond-mediated aglycon delivery system provides a reliable method for the synthesis of challenging phenolic glycosides. In addition, a chemoselective glycosylation procedure was developed using different imidate donors (trichloroacetimidates, N-phenyl trifluoroacetimidates, N-4-nitrophenyl trifluoroacetimidates, benzoxazolyl imidates and 6-nitro-benzothiazolyl imidates) and it was applied for a trisaccharide synthesis through a novel one-pot single catalyst strategy.

A mild glycosylation system was developed using glycosyl imidate donors and a charge-enhanced thiourea H-bond donor catalyst. The method can be used for the effective synthesis of O-, C-, S- and N-glycosides and chemoselective one-pot glycosylation.

Organocatalysis applied to carbohydrates: from roots to current developments

Organocatalysis emerged in the last decade as a powerful tool for the synthesis of complex molecules. In the field of carbohydrates, it found widespread use in the synthesis of rare and non-natural carbohydrate derivatives. Additionally, it has also found important application in the stereoselective functionalization of the anomeric carbon in glycosylation reactions. These efforts culminated in the development of different types of catalysts operating through distinct activation modes that allow the selective synthesis of α- or β-glycosides even on daunting substrates. All these advances starting from its first examples in carbohydrate synthesis to the current developments in glycosylation reactions are reviewed.

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.

Enantio- and diastereoselective double Mannich reaction of malononitrile with N-Boc imines using quinine-derived bifunctional organoiodine catalyst

A chiral quinine-derived organic base catalyst with halogen bond donor functionality was used to catalyze the asymmetric double Mannich reaction of malononitrile with N-Boc and N-Cbz imines to afford 1,3-diamines in excellent yields with high enantio- and diastereoselectivities. With 2.2 equiv. of a single imine electrophile, symmetrical 1,3-diamines were obtained, whereas, with two different imine partners, unsymmetrically substituted 1,3-diamine was obtained. The monohydration of the double Mannich product was also achieved.

Self-Promoted Stereoselective Glycosylations - Past, Present, Future

Self-promoted glycosylations have generally not received much attention, despite having the advantages of being easy to perform and often highly stereoselective. This account covers the work done in this field and the mechanistic aspects of self-promoted glycosylations are discussed, with a main focus on the stereoselectivity of the reactions. Most self-promoted glycosylations utilize trichloroacetimidate donors, but examples of self-promoted reactions with other donors have been described and will be discussed. Self-promoted glycosylation strategies can provide a basis for new stereoselective glycosylation methodologies.

Synthesis of 4-Cyanoindole Nucleosides, 4-Cyanoindole-2'-Deoxyribonucleoside-5'-Triphosphate (4CIN-TP), and Enzymatic Incorporation of 4CIN-TP into DNA

4-Cyanoindole-2'-deoxyribonucleoside (4CIN) is a fluorescent isomorphic nucleoside analogue with superior spectroscopic properties in terms of Stokes shift and quantum yield in comparison to the widely utilized isomorphic nucleoside analogue, 2-aminopurine-2'-deoxyribonucleoside (2APN). Notably, when inserted into single- or double-stranded DNA, 4CIN experiences substantially less in-strand fluorescence quenching compared to 2APN. Given the utility of these properties for a spectrum of research applications involving oligonucleotides and oligonucleotide-protein interactions (e.g., enzymatic processes, DNA hybridization, DNA damage), we envision that additional reagents based on 4-cyanoindole nucleosides may be widely utilized. This protocol expands on the previously published synthesis of 4CIN to include synthetic routes to both 4-cyanoindole-ribonucleoside (4CINr) and 4-cyanoindole-2'-deoxyribonucleoside-5'-triphosphate (4CIN-TP), as well as a method for the enzymatic incorporation of 4CIN-TP into DNA by a polymerase. These methods are anticipated to further enable the utilization of 4CIN in diverse applications involving DNA and RNA oligonucleotides. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of 4-cyanoindole-2'-deoxyribonucleoside (4CIN) and 4CIN phosphoramidite 4 Basic Protocol 2: Synthesis of 4-cyanoindole-ribonucleoside (4CINr) Basic Protocol 3: Synthesis of 4-cyanoindole-2'-deoxyribonucleoside-5'-triphosphate (4CIN-TP) Basic Protocol 4: Steady state incorporation kinetics of 2AP-TP and 4CIN-TP by a DNA polymerase.

A Hypervalent Cyclic Dibenzoiodolium Salt as a Halogen-Bond-Donor Catalyst for the [4+2] Cycloaddition of 2-Alkenylindoles

A stable, hypervalent cyclic dibenzoiodolium salt acted as a strong halogen bonding (XB)-donor catalyst for [4+2] cycloaddition of 2-alkenylindoles, and not as an oxidizing agent. The cross-[4+2] cycloaddition of 2-vinylindoles with 2-alkenylindoles was catalyzed smoothly by the hypervalent cyclic dibenzoiodolium triflate catalyst to give the tetrahydrocarbazoles in up to 99 % yield with 17 : 1 diastereoselectivity. The hypervalent cyclic dibenzoiodolium salt was also applicable to the Povarov reaction of 2-vinylindole with N-p-methoxyphenyl (PMP) imine to give the indolyl-tetrahydroquinoline in 83 % yield.

One step stereoselective synthesis of oxazoline-fused saccharides and their conversion into the corresponding 1,2-cis glycosylamines bearing various protected groups

Herein we disclosed a straightforward synthesis of oxazoline-fused saccharides (oxazolinoses) from peracetylated saccharides and benzonitriles under acidic conditions with stoichiometric amounts of water. The density functional theory (DFT) calculations have revealed the origin of the stereoselectivity and the key role of water in promoting the departure of the acetyl group at C-2. The resulting oxazolinoses can be concisely converted into the corresponding 1,2-cis glycosylamines bearing various protected groups, allowing the access to schisandrin derivatives.

Azolium/Hydroquinone Organo-Radical Co-Catalysis: Aerobic C-C-Bond Cleavage in Ketones

Organo-radical catalysts have recently attracted great interest, and the development of this field can be expected to broaden the applications of organocatalysis. Herein, the first example of a radical-generating system is reported that does not require any photoirradiation, radical initiators, or preactivated substrates. The oxidative C-C-bond cleavage of 2-substituted cyclohexanones was achieved using an azolium salt and a hydroquinone as co-catalysts. A catalytic mechanism was proposed based on the results of diffusion-ordered spectroscopy and cyclic voltammetry measurements, as well as computational studies.

Bromonium salts: diaryl-λ3-bromanes as halogen-bonding organocatalysts

Bromonium salts have been typically but infrequently used as good leaving groups owing to their high nucleofugality. Herein, we report the synthesis of stable bromonium salts and their first catalytic application, with excellent product yield.

Brønsted acid-catalyzed dynamic kinetic resolution of in situ formed acyclic N,O-hemiaminals: cascade synthesis of chiral cyclic N,O-aminals

A H2O controlled dynamic kinetic resolution was involved in a Brønsted acid-catalyzed acyclic N,O-hemiaminal formation/oxa-Michael reaction cascade, leading to highly enantioenriched cis-2,6-disubstituted tetrahydropyrans bearing an exo amide group.

Direct N-glycosylation of tosyl and nosyl carbamates with trichloroacetimidate donors

Acidic sulphonamide reactants act as both catalysts and nucleophiles to afford the desired N-glycofuranosyl sulfonamides stereoselectively.

Influence of Anion-Binding Schreiner's Thiourea on DMAP Salts: Synergistic Catalysis toward the Stereoselective Dehydrative Glycosylation from 2-Deoxyhemiacetals

Amines are used as additives to facilitate or increase the host-guest chemistry between the thiourea and the anions of Bronsted acids. However, we here demonstrate, for the first time, the synergistic effect of the combination of DMAP/HCl/Schreiner's thiourea in catalyzing dehydrative glycosylation. The variations in the electronic effects of the cationic Bronsted acid part (the protonated DMAP) in the presence of chloride binding Schreiner's thiourea have been discussed using NMR and X-ray crystallographic techniques.

A robust and tunable halogen bond organocatalyzed 2-deoxyglycosylation involving quantum tunneling

The development of noncovalent halogen bonding (XB) catalysis is rapidly gaining traction, as isolated reports documented better performance than the well-established hydrogen bonding thiourea catalysis. However, convincing cases allowing XB activation to be competitive in challenging bond formations are lacking. Herein, we report a robust XB catalyzed 2-deoxyglycosylation, featuring a biomimetic reaction network indicative of dynamic XB activation. Benchmarking studies uncovered an improved substrate tolerance compared to thiourea-catalyzed protocols. Kinetic investigations reveal an autoinductive sigmoidal kinetic profile, supporting an in situ amplification of a XB dependent active catalytic species. Kinetic isotopic effect measurements further support quantum tunneling in the rate determining step. Furthermore, we demonstrate XB catalysis tunability via a halogen swapping strategy, facilitating 2-deoxyribosylations of D-ribals. This protocol showcases the clear emergence of XB catalysis as a versatile activation mode in noncovalent organocatalysis, and as an important addition to the catalytic toolbox of chemical glycosylations.

Halogen bonding (HB) catalysis is rapidly gaining momentum, however, cases of XB activation for challenging bonds formation are rare. Here, the authors show a robust XB catalyzed 2-deoxyglycosylation with broad scope and featuring a quantum tunneling phenomenon in the proton transfer rate determining step.

Direct N-Glycosylation of Amides/Amines with Glycal Donors

Direct N-glycosylation between glycals and amides/amines was achieved with exclusive stereoselectivity in moderate to high yields. Various amides, amines, and 3,4-O-carbonate-glycals were tolerated, and unique β-N-glycosides were obtained. The strategy was based on palladium-catalyzed decarboxylative allylation, and the high 1,4-cis-selectivity was proposed because of the hydrogen bonding effect. Notably, all the synthesized products were subjected to preliminary bioactivity studies, revealing that three compounds were cytotoxic to tumor cells and nontoxic to normal human cells.

Stereospecific Furanosylations Catalyzed by Bis-thiourea Hydrogen-Bond Donors

We report a new method for stereoselective O-furanosylation reactions promoted by a precisely tailored bis-thiourea hydrogen-bond-donor catalyst. Furanosyl donors outfitted with an anomeric dialkylphosphate leaving group undergo substitution with high anomeric selectivity, providing access to the challenging 1,2-cis substitution pattern with a range of alcohol acceptors. A variety of stereochemically distinct, benzyl-protected glycosyl donors were engaged successfully as substrates. Mechanistic studies support a stereospecific mechanism in which rate-determining substitution occurs from a catalyst-donor resting-state complex.

Lewis acid–base synergistic catalysis of cationic halogen-bonding-donors with nucleophilic counter anions

1,3,4-Triaryl-5-iodotriazolium iodides have been developed as halogen-bonding based bifunctional catalysts for simultaneous activation of nucleophiles and electrophiles.