Poor Nucleophiles Research Articles

Base-Promoted Coupling of HFIP in Cu-Catalyzed Asymmetric Ring Opening of Cyclic Diaryliodoniums.

We report a Cu-catalyzed asymmetric ring-opening reaction of cyclic diaryliodoniums with 1,1,1,3,3,3-hexafluoroisopropanol (HFIP), enabling the construction of axially chiral biaryl compounds containing HFIP ether. HFIP is highly polar and exceptionally stable; thus, it is commonly used as a solvent due to its poor nucleophilicity. However, its use as a nucleophilic reagent has been rare. In this study, we successfully employed HFIP as a nucleophilic coupling partner in a Cu-catalyzed asymmetric ring-opening experiment of cyclic diaryliodoniums.

Activity and Biocatalytic Potential of an Indolylamide Generating Thioesterase.

The chemical synthesis of N-acyl indoles is hindered by the poor nucleophilicity of indolic nitrogen, necessitating the use of strongly basic reaction conditions that encumber elaboration of highly functionalized scaffolds. Herein, we describe the total chemoenzymatic synthesis of the bulbiferamide natural products by the biochemical activity reconstitution of a nonribosomal peptide synthetase assembly line-derived (NRPS-derived) thioesterase that neatly installs the macrocyclizing indolylamide. The enzyme represents a starting point for biocatalytic access to macrocyclic indolylamide peptides and natural products.

Understanding Nucleophilicity of Pyridine-N-oxides Towards 2,4,6-Trinitrophenylbenzoate Through Simple Absorption Spectroscopic Studies

Aims: Understanding nucleophilicity of poor nucleophiles like pyridine-N-oxides. Background: Nucleophilicity plays a vital role in substitution reactions. It helps to determine the possibility and extent of the substitution reactions. The study of the nucleophilicity of poor nucleophiles is challenging, and it has limited substrate scope. Understanding the strength of nucleophilicity of such poor nucleophiles in a quantitative way is important. Objective: Understanding the strength of nucleophilicity of such poor nucleophiles in a quantitative way. Selection of appropriate electrophile for the reactions with the poor nucleophiles-pyridine-N-oxides. Development of suitable methodology for kinetic studies of the reaction. Methods: UV-Vis spectroscopic methods for monitoring the reactions. Results: The kinetic studies revealed that the second-order rate constants of the nucleophilic reactions are 1.67× 102 L mol-1 min-1, 29.8 L mol-1 min-1, 29.51 L mol-1 min-1, where the nucleophiles are p-methylpyridine-N-oxide, pyridine-N-oxide, and p-nitropyridine-N-oxide, respectively. The UV-Vis spectroscopic analysis revealed the nucleophilicity of p-methylpyridine-N-oxide > pyri-dine-N-oxide > p-nitropyridine-N-oxide. Conclusion: This comparative study suggests that the strength of nucleophilicity of the p-methylpyridine-N-oxide is 5.6 times and 66.53 times more than that of pyridine-N-oxide and p-nitropyridine-N-oxide, respectively, whereas the strength of nucleophilicity of the pyridine-N-oxide is 11.87 times more than that of p-nitropyridine-N-oxide.

Co-Catalyzed Hydrofluorination of Alkenes: Photocatalytic Method Development and Electroanalytical Mechanistic Investigation.

The hydrofluorination of alkenes represents an attractive strategy for the synthesis of aliphatic fluorides. This approach provides a direct means to form C(sp3)-F bonds selectively from readily available alkenes. Nonetheless, conducting hydrofluorination using nucleophilic fluorine sources poses significant challenges due to the low acidity and high toxicity associated with HF and the poor nucleophilicity of fluoride. In this study, we present a new Co(salen)-catalyzed hydrofluorination of simple alkenes utilizing Et3N·3HF as the sole source of both hydrogen and fluorine. This process operates via a photoredox-mediated polar-radical-polar crossover mechanism. We also demonstrated the versatility of this method by effectively converting a diverse array of simple and activated alkenes with varying degrees of substitution into hydrofluorinated products. Furthermore, we successfully applied this methodology to 18F-hydrofluorination reactions, enabling the introduction of 18F into potential radiopharmaceuticals. Our mechanistic investigations, conducted using rotating disk electrode voltammetry and DFT calculations, unveiled the involvement of both carbocation and CoIV-alkyl species as viable intermediates during the fluorination step, and the contribution of each pathway depends on the structure of the starting alkene.

Total Synthesis of a Conjugation-Ready Tetrasaccharide Repeating Unit of Vibrio cholerae O:3 O-antigen Polysaccharide.

Herein, we report the first total synthesis of the tetrasaccharide repeating unit of Vibrio cholerae O:3 O-antigen polysaccharide. The highly complex tetrasaccharide contains rare amino sugars such as d-bacillosamine and l-fucosamine, highly labile sugar ascarylose, and higher carbon sugar d-d-heptose. Stereoselective glycosylation of the notoriously reactive ascarylose with d-d-heptose, poor nucleophilicity of the axial C4-OH of l-fucosamine, and amide coupling are the key challenges encountered in the total synthesis, which was completed via a longest linear sequence of 23 steps in 4.2% overall yield.

Multicomponent Dearomative Difluoroalkylation of Isoquinolines with Difluorinated Silyl Enol Ethers: Divergent Synthesis of gem-Difluorinated Heterocycles.

A multicomponent dearomative difluoroalkylation of isoquinolines has been developed with difluorinated silyl enol ethers serving as poor nucleophiles without an additional transition-metal or organic catalyst. The sequential oxidative rearomatization under different alkaline conditions provides a controllable formal C-H difluoroalkylation and difluoromethylation method for isoquinolines without peroxide or metal oxidant. A series of isoquinolines including a pharmaceutical, phenanthridine, quinolines, and difluorinated silyl enol ethers were suitable substrates to construct gem-difluorinated heterocycles. The inexpensive starting materials, mild reaction conditions, and simple operation also show practical and environmentally benign advantages.

“Stereoelectronic Deprotection of Nitrogen”: Recovering Nucleophilicity with a Conformational Change

Ureas are often thought of as "double amides" due to the obvious structural similarity of these functional groups. The main structural feature of an amide is its planarity, which is responsible for the conjugation between the nitrogen atom and carbonyl moiety and the decrease of amide nucleophilicity. Consequently, since amides are poor nucleophiles, ureas are often thought of as poor nucleophiles as well. Herein, we demonstrate that ureas can be distinctly different from amides. These differences can be amplified by rotation around one of the ureas' C-N bonds, which switches off the amide resonance and recovers the nucleophilicity of one of the nitrogen atoms. This conformational change can be further facilitated by the judicious introduction of steric bulk to disfavor the planar conformation. This change in reactivity is an example of "stereoelectronic deprotection," a concept when the desired reactivity of a functional group is produced by a conformational change rather than a chemical modification. This concept may be used complementarily to the traditional protecting groups. We also demonstrate both the viability and the utility of this concept by the synthesis of unusual 2-oxoimidazolium salts possessing quaternary nitrogen atoms at the urea moiety.

Efficient Monoalkylation of Anilines with Chalcones using Microwave-Assisted aza-Michael Addition

Abstract: The aza-Michael addition is an attractive methodology for synthetic organic chemistry because the resulting β-aminocarbonyl compounds are valuable building blocks for the synthesis of pharmaceutically useful compounds. However, monoalkylation of aniline and its derivatives is quite difficult because anilines are poor nucleophiles compared to monoalkylated ones. Since the publication of pioneering articles in 1986, the development of microwave-assisted organic synthesis has been remarkable. Therefore, we began by investigating the monoalkylation of aniline and its derivatives under microwave irradiation. Because of the ready formation of bisalkylated products, the monoalkylation reaction between anilines and Michael acceptors is quite difficult. To overcome the difficulty, we investigated the effect of microwave irradiation for the alkylation of anilines with chalcones as Michael acceptors. Microwave-assisted aza-Michael addition proceeded smoothly to obtain mainly the monoalkylated Michael adduct. The substitution effects of both chalcone and aniline concerning the yield were also studied. We supposed that dimer formation by two monoalkylated compounds produces a bulky environment around the amino group, which prevents monoalkylated compounds from undergoing a second alkylation. We confirmed a highly efficient and rapid method for preparing monoalkylated anilines using microwave-assisted aza-Michael addition between anilines and chalcones.

Donor-Acceptor Pyridinium Salts for Photo-Induced Electron-Transfer-Driven Modification of Tryptophan in Peptides, Proteins, and Proteomes Using Visible Light.

Tryptophan (Trp) plays a variety of critical functional roles in protein biochemistry; however, owing to its low natural frequency and poor nucleophilicity, the design of effective methods for both single protein bioconjugation at Trp as well as for in situ chemoproteomic profiling remains a challenge. Here, we report a method for covalent Trp modification that is suitable for both scenarios by invoking photo-induced electron transfer (PET) as a means of driving efficient reactivity. We have engineered biaryl N-carbamoyl pyridinium salts that possess a donor-acceptor relationship that enables optical triggering with visible light whilst simultaneously attenuating the probe's photo-oxidation potential in order to prevent photodegradation. This probe was assayed against a small bank of eight peptides and proteins, where it was found that micromolar concentrations of the probe and short irradiation times (10-60 min) with violet light enabled efficient reactivity toward surface exposed Trp residues. The carbamate transferring group can be used to transfer useful functional groups to proteins including affinity tags and click handles. DFT calculations and other mechanistic analyses reveal correlations between excited state lifetimes, relative fluorescence quantum yields, and chemical reactivity. Biotinylated and azide-functionalized pyridinium salts were used for Trp profiling in HEK293T lysates and in situ in HEK293T cells using 440 nm LED irradiation. Peptide-level enrichment from live cell labeling experiments identified 290 Trp modifications, with 82% selectivity for Trp modification over other π-amino acids, demonstrating the ability of this method to identify and quantify reactive Trp residues from live cells.

A photoredox-catalyzed approach for formal hydride abstraction to enable Csp3–H functionalization with nucleophilic partners (F, C, O, N, and Br/Cl)

A catalytic Csp3–H functionalization manifold for accessing reactive carbocation intermediates directly from a range of Csp3–H bonds is reported. The catalytic design relies on a strategy driven by visible-light photoredox catalysis that combines two mechanistic steps in one catalytic cycle: hydrogen-atom transfer (HAT) and radical-polar crossover (RPC), representing a net hydride abstraction. We herein demonstrate a mild and robust [HAT + RPC] platform that can efficiently enable a Csp3–H fluorination with nucleophilic fluoride—a classically poor nucleophile. Notably, the [HAT + RPC] protocol was successful in the late-stage fluorination of several commercial drugs. Difluorination of methylene groups is also demonstrated, and represents the first C–H difluorination with nucleophilic fluoride. Importantly, long-term potential of the design was demonstrated with the engagement of other nucleophile classes including halides, alcohols, water, N-heterocycle, carboxylic acids, azide, and arenes, thus showcasing its potential as a unified C–H functionalization method.

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 SN 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.

A New Saddle-Shaped Aza Analog of Tetraphenylene: Atroposelective Synthesis and Application as a Chiral Acylating Reagent

A New Saddle-Shaped Aza Analog of Tetraphenylene: Atroposelective Synthesis and Application as a Chiral Acylating Reagent

A Fischer-Type Ruthenium Carbene Complex as a Metathesis Catalyst for the Synthesis of Enol Ethers.

The Grubbs G-I or G-II catalyst gives the ruthenium ethoxy carbene complex, which catalyzes ring-opening cross metathesis (ROCM) of a strained cyclic alkene to give a diene where one of the two alkene moieties in the product contains an ethoxy substituent. No polymeric products are detected. Hydrocarbons such as parent norbornene or substituted cyclopropenes can proceed with the reaction smoothly. Tertiary amines, N-alkylimides, esters, and aryl or alkyl bromides remain intact under the reaction conditions. In addition to vinyl ethers, vinylic esters can also be used. The time required to reach a 50% yield of the ROCM product t50 varies from 0.01 to 140 h depending on the strain and nucleophilicity of the double bond. Anchimeric participation of an electron-rich group would result in significant enhancement of the reactivity, and the t50 could be as short as several minutes. A similar substrate without such a neighboring group shows a much slower rate. An exo-norborne derivative reacts much faster than the corresponding endo-isomer. Alkenes with poor nucleophilicity are less favored for the ROCM process, so is less strained cyclooctene.

Total Synthesis of the All-Rare Sugar-Containing Pentasaccharide Repeating Unit of the O-Polysaccharide of Plesiomonas shigelloides Strain 302-73 (Serotype O1).

First total synthesis of the conjugation-ready pentasaccharide repeating unit of Plesiomonas shigelloides strain 302-73 (serotype O1) is reported. The complex target pentasaccharide is composed of all-rare amino sugars such as orthogonally functionalized d-bacillosamine, l-fucosamine, and l-pneumosamine linked through four consecutive α-linkages. The poor nucleophilicity of axial 4-OH of l-fucosamine and stereoselective glycosylations are the key challenges in the total synthesis, which was completed via a longest linear sequence of 27 steps in 3% overall yield.

Transition Path Sampling Study of the Feruloyl Esterase Mechanism.

Serine hydrolases cleave peptide and ester bonds and are ubiquitous in nature, with applications in biotechnology, in materials, and as drug targets. The serine hydrolase two-step mechanism employs a serine-histidine-aspartate/glutamate catalytic triad, where the histidine residue acts as a base to activate poor nucleophiles (a serine residue or a water molecule) and as an acid to allow the dissociation of poor leaving groups. This mechanism has been the subject of debate regarding how histidine shuttles the proton from the nucleophile to the leaving group. To elucidate the reaction mechanism of serine hydrolases, we employ quantum mechanics/molecular mechanics-based transition path sampling to obtain the reaction coordinate using the Aspergillus niger feruloyl esterase A (AnFaeA) as a model enzyme. The optimal reaction coordinates include terms involving nucleophilic attack on the carbonyl carbon and proton transfer to, and dissociation of, the leaving group. During the reaction, the histidine residue undergoes a reorientation on the time scale of hundreds of femtoseconds that supports the "moving histidine" mechanism, thus calling into question the "ring flip" mechanism. We find a concerted mechanism, where the transition state coincides with the tetrahedral intermediate with the histidine residue pointed between the nucleophile and the leaving group. Moreover, motions of the catalytic aspartate toward the histidine occur concertedly with proton abstraction by the catalytic histidine and help stabilize the transition state, thus partially explaining how serine hydrolases enable poor nucleophiles to attack the substrate carbonyl carbon. Rate calculations indicate that the second step (deacylation) is rate-determining, with a calculated rate constant of 66 s-1. Overall, these results reveal the pivotal role of active-site dynamics in the catalytic mechanism of AnFaeA, which is likely similar in other serine hydrolases.

Ribosomal Elongation of Aminobenzoic Acid Derivatives.

2-Aminobenzoic acid and heterocyclic amino acids are aromatic homologues of β-amino acids, but their chemical properties are quite distinct. Because of the poor nucleophilicity of the amino group conjugated with the aromatic ring, no literature reports of their successful ribosomal elongation in nascent peptide chains have appeared to date. Here we report for the first time their incorporation in nascent peptide chains by means of a reconstituted translation system in which a designer tRNAPro1E2 capable of recruiting the elongation factors EF-Tu and EF-P was charged with their derivatives and the corresponding peptides were successfully expressed. We also demonstrate the expression of macrocyclic peptides containing exotic amino acids, including aminobenzoic acid derivatives.

Bacteria-Catalyzed Arginine Glycosylation in Pathogens and Host

In recent years, protein glycosylation in pathogenic bacteria has attracted more and more attention, and accumulating evidence indicated that this type of posttranslational modification is involved in many physiological processes. The NleB from several enteropathogenic bacteria species as well as SseK from Salmonella enterica are type III secretion system effectors, which have an atypical N-acetylglucosamine (N-GlcNAc) transferase activity that specifically modified a conserved arginine in TRADD, FADD, and RIPK1. NleB/SseKs GlcNAcylation of death domain proteins abrogates homotypic and heterotypic death receptors/adaptors interactions, thereby blocking an important antimicrobial host response. Interestingly, NleB/SseKs could also GlcNAcylate themselves, and self-GlcNAcylation of NleB, SseK1, and SseK3 are crucial for their biological activity during infection. In addition, EarP (EF-P specific arginine rhamnosyl transferase for Posttranslational activation) catalyzes arginine rhamnosylation of translation elongation factor P (EF-P). Importantly, this kind of N-linked protein glycosylation is not only important for EF-P dependent rescue of polyproline stalled ribosomes but also for pathogenicity in Pseudomonas aeruginosa and other clinically relevant bacteria. Glycosylation of arginine is unique because the guanidine group of arginine has a high acid dissociation constant value and representing an extremely poor nucleophile. Recently, the crystal structures of NleB, SseKs, EarP, arginine GlcNAcylated death domain-containing proteins, NleB/FADD-DD, and EarP/EF-P/dTDP-β-L-rhamnose were solved by our group and other groups, revealing the unique catalytic mechanisms. In this review, we provide detailed information about the currently known arginine glycosyltransferases and their potential catalytic mechanisms.

Structural and Computational Analysis of 2‐Halogeno‐Glycosyl Cations in the Presence of a Superacid: An Expansive Platform

AbstractAn expansive NMR‐based structural analysis of elusive glycosyl cations derived from natural and non‐natural monosaccharides in superacids is disclosed. For the first time, it has been possible to explore the consequence of deoxygenation and halogen substitution at the C2 position in a series of 2‐halogenoglucosyl, galactosyl, and mannosyl donors in the condensed phase. These cationic intermediates were characterized using low‐temperature in situ NMR experiments supported by DFT calculations. The 2‐bromo derivatives display intramolecular stabilization of the glycosyl cations. Introducing a strongly electron‐withdrawing fluorine atom at C2 exerts considerable influence on the oxocarbenium ion reactivity. In a superacid, these oxocarbenium ions are quenched by weakly coordinating SbF6− anions, thereby demonstrating their highly electrophilic character and their propensity to interact with poor nucleophiles.

Structural and Computational Analysis of 2-Halogeno-Glycosyl Cations in the Presence of a Superacid: An Expansive Platform.

An expansive NMR-based structural analysis of elusive glycosyl cations derived from natural and non-natural monosaccharides in superacids is disclosed. For the first time, it has been possible to explore the consequence of deoxygenation and halogen substitution at the C2 position in a series of 2-halogenoglucosyl, galactosyl, and mannosyl donors in the condensed phase. These cationic intermediates were characterized using low-temperature in situ NMR experiments supported by DFT calculations. The 2-bromo derivatives display intramolecular stabilization of the glycosyl cations. Introducing a strongly electron-withdrawing fluorine atom at C2 exerts considerable influence on the oxocarbenium ion reactivity. In a superacid, these oxocarbenium ions are quenched by weakly coordinating SbF6- anions, thereby demonstrating their highly electrophilic character and their propensity to interact with poor nucleophiles.

Structural Basis of Tryptophan Reverse N-Prenylation Catalyzed by CymD.

Indole prenyltransferases catalyze the prenylation of l-tryptophan (l-Trp) and other indoles to produce a diverse set of natural products in bacteria, fungi, and plants, many of which possess useful biological properties. Among this family of enzymes, CymD from Salinispora arenicola catalyzes the reverse N1 prenylation of l-Trp, an unusual reaction given the poor nucleophilicity of the indole nitrogen. CymD utilizes dimethylallyl diphosphate (DMAPP) as the prenyl donor, catalyzing the dissociation of the diphosphate leaving group followed by nucleophilic attack of the indole nitrogen at the tertiary carbon of the dimethylallyl cation. To better understand the structural basis of selective indole N-alkylation reactions in biology, we have determined the X-ray crystal structures of CymD, the CymD-l-Trp complex, and the CymD-l-Trp-DMSPP complex (DMSPP is dimethylallyl S-thiolodiphosphate, an unreactive analogue of DMAPP). The orientation of l-Trp with respect to DMSPP reveals how the active site contour of CymD serves as a template to direct the reverse prenylation of the indole nitrogen. Comparison to PriB, a C6 bacterial indole prenyltransferase, offers further insight regarding the structural basis of regioselective indole prenylation. Isothermal titration calorimetry measurements indicate a synergistic relationship between l-Trp and DMSPP binding. Finally, activity assays demonstrate the selectivity of CymD for l-Trp and indole as prenyl acceptors. Collectively, these data establish a foundation for understanding and engineering the regioselectivity of indole prenylation by members of the prenyltransferase protein family.