Twisted Amide Research Articles

Twisted Amide-Mediated Peptide Synthesis.

A robust, practical, and sustainable isomerization-suppressed peptide bond formation via acyl sulfonamide, a twisted amide, is disclosed. Tosyl isocyanate and pentafluorobenzyl bromide were applied in combination to activate the peptide C-terminus, which then reacted with an amine to yield an elongated peptide with high stereochemical purity. Careful analysis of NMR spectra of the active intermediate revealed the presence of an intramolecular hydrogen bond, suggesting that the hydrogen bond suppressed Cα-epimerization during amidation. The isomerization suppression by the intramolecular hydrogen bond is expected to be effective even under high dilution conditions, making the present method a powerful tool for the synthesis of complex macrocyclic peptides. In addition to peptide synthesis, the developed synthetic entry to twisted amides can be applied to the investigation of transition metal-catalyzed N-C bond activation. Moreover, the application to the N-C bond activation returned insight into peptide synthesis, leading to the use of sulfonamide as a protecting group of carboxylic acid that can be orthogonally removed in the presence of other conventional protecting groups.

Halide Abstraction-Mediated Synthesis of a Highly Twisted Amide.

Highly strained [3.2.1] bicyclic twisted amide 2 and corresponding amidium 10 were synthesized for the first time through Ag(I)-mediated halide abstraction. After initial lactamization attempts failed, a second-generation strategy was devised to target amidium 10 via intramolecular alkylation. The 3,4-dihydroisoquinolone cyclization precursor was regioselectively prepared via a Rh(III)-catalyzed C-H activation/annulation reaction. After Ag(I)-assisted cyclization, the [3.2.1] bicyclic framework of amidium 10 was confirmed by X-ray crystallography and enabled full solution characterization of twisted amide 2.

Modulating Twisted Amide Geometry and Reactivity Through Remote Substituent Effects.

The unusual reactivity of twisted amides has long been associated with the degree of amide distortion, though classical bridged bicyclic amides offer limited methods to further modify these parameters. Here, we report that the geometry and reactivity of a single twisted amide scaffold can be significantly modulated through remote substituent effects. Guided by calculated ground state geometries, a library of twisted amide derivatives was efficiently prepared through a divergent synthetic strategy. Kinetic and mechanistic investigations of these amides in the alkylation/halide-rebound ring-opening reaction with alkyl halides show a strong positive correlation between the electron donating ability of the substituent and distortion of the amide bond, leading to rates of nucleophilic substitution spanning nearly 2 orders of magnitude. The rate limiting step of the cascade sequence is found to be dependent on the nature of the substituent, and additional studies highlight the role of solvent polarity and halide ion on reaction pathway and efficiency.

Evaluation of Cyclic Amides as Activating Groups in N-C Bond Cross-Coupling: Discovery of N-Acyl-δ-valerolactams as Effective Twisted Amide Precursors for Cross-Coupling Reactions.

The development of efficient methods for facilitating N-C(O) bond activation in amides is an important objective in organic synthesis that permits the manipulation of the traditionally unreactive amide bonds. Herein, we report a comparative evaluation of a series of cyclic amides as activating groups in amide N-C(O) bond cross-coupling. Evaluation of N-acyl-imides, N-acyl-lactams, and N-acyl-oxazolidinones bearing five- and six-membered rings using Pd(II)-NHC and Pd-phosphine systems reveals the relative reactivity order of N-activating groups in Suzuki-Miyaura cross-coupling. The reactivity of activated phenolic esters and thioesters is evaluated for comparison in O-C(O) and S-C(O) cross-coupling under the same reaction conditions. Most notably, the study reveals N-acyl-δ-valerolactams as a highly effective class of mono-N-acyl-activated amide precursors in cross-coupling. The X-ray structure of the model N-acyl-δ-valerolactam is characterized by an additive Winkler-Dunitz distortion parameter Σ(τ+χN) of 54.0°, placing this amide in a medium distortion range of twisted amides. Computational studies provide insight into the structural and energetic parameters of the amide bond, including amidic resonance, N/O-protonation aptitude, and the rotational barrier around the N-C(O) axis. This class of N-acyl-lactams will be a valuable addition to the growing portfolio of amide electrophiles for cross-coupling reactions by acyl-metal intermediates.

Tuning the electronic effects in designing ligands for the inhibition of rotamase activity of FK506 binding protein

FK506-binding protein (FKBP) is a cytosolic enzyme, which catalyzes the cis–trans isomerization of prolyl peptides. The twisted amide geometries assist the isomerization process and inhibit the rotamase activity of FKBP. This work reveals the role of electronic effects in ligands to facilitate the twisted amide geometries for efficient inhibition of the rotamase activity of FKBP12. The azirine ligand (5A) lowered the rotation barrier of –C–N amide bond by ~ 14.0 kcal/mol compared to the reference ligand molecule (1A) using M062X/cc-pVDZ//M062X/6-31G(d) level of theory. A significant lowering in rotation barrier has been achieved in (5A) due to the ring's anti-aromatic nature. The ring strain in the 1H-azirine ring pyramidalizes the amide bond's nitrogen center by 78° in the ground state compared to 1A. The natural bond orbital (NBO) analysis confirmed the lowering in the delocalization of electron density from nitrogen lone pair to π*C = O orbital in amide bonds. The designed models (1A-5A) were developed into ligands to mimic the binding domain of FK506 (1B-5B). The binding of these ligands (1B-5B) was examined with the quantum mechanics and molecular mechanics (QM/MM) ONIOM approach in the presence of FKBP12 binding site residues. The calculated results reveal the preferential binding of twisted amide forms with FKBP12 over their planar analogous. The hydrophobic interactions augment the binding affinity of the twisted forms with the FKBP12 binding site in agreement with the experimental observations. These studied ligands could act as potential inhibitors of FKBP12 for their therapeutic application.

Ring-Opening Olefin Metathesis of Twisted Amides: Activation of Amide Bonds by C═C Cleavage

Selective C═C bond cleavage in twisted amides by ring-opening olefin metathesis (ROM) was accomplished. The reaction represents the third mechanism for ring opening of nonplanar amide bonds discovered. Adding to the facile hydrolytic cleavage of nonplanar N–C(O) amide bonds and σ N–C bond scission reactions, this reaction manifold engages a peripheral reactivity principle that hinges upon ring strain energy enforced by the twisted amide bond. Considering the wide utility of ring-opening olefin metathesis reactions in various aspects of chemistry, we anticipate that this ring-opening methodology will be of broad interest and could lead to the development of ROM reactions of twisted amides as a powerful synthetic tool.

Investigations of an annulation-fragmentation-spirocyclisation approach to fawcettimine-type Lycopodium alkaloids

This paper reports progress in the development of a furan oxidative N-spirocyclisation approach to the fawcettimine alkaloids huperzine Q and lycopladine D. A short synthesis is described of a key intermediate cyclopentaindolizidine that subsequently fragments by N-acylation and β-elimination. The stereochemistry of 1,4-addition of cyanide to the resulting enone is discussed with supporting molecular modelling calculations. N-Deprotection is shown to be accompanied by cyclisation onto the nitrile group, resulting in a tricyclic lactam with a twisted amide functionality. Elaboration of this lactam afforded four of the five rings present in lycopladine D with just the C(8) carbon lacking.

Synthesis of Quaternary Carbon-Centered Benzoindolizidinones via Novel Photoredox-Catalyzed Alkene Aminoarylation: Facile Access to Tylophorine and Analogues

Photoredox-catalyzed aminoarylation and thioamination of unactivated alkenes have been developed, providing novel synthetic routes to access synthetically challenging quaternary carbon-centered ben...

Structure and Reactivity of Highly Twisted N-Acylimidazoles.

A modular and efficient synthesis of highly twisted N-acylimidazoles is reported. These twist amides were characterized via X-ray crystallography, NMR spectroscopy, IR spectroscopy, and DFT calculations. Modification of the substituent proximal to the amide revealed a maximum torsional angle of 88.6° in the solid state, which may be the most twisted amide reported for a nonbicyclic system to date. Reactivity and stability studies indicate that these twisted N-acylimidazoles may be valuable, namely as acyl transfer reagents.

Halide-Rebound Polymerization of Twisted Amides.

The first living polymerization of twisted amides is reported, achieved using simple primary alkyl iodides as initiators. Polymerization occurs through a halide-rebound mechanism in which the nucleophilic twisted amide is quaternized and subsequently ring-opened by the iodide counterion. The covalent electrophilic polymerization generates polymers with living chain ends that are both isolable and stable to ambient conditions, enabling the synthesis of block polymers. This presents a new class of polymers for study that possess high glass transition temperatures and robust thermal stability.

Fast Amide Bond Cleavage Assisted by a Secondary Amino and a Carboxyl Group-A Model for yet Unknown Peptidases?

Unconstrained amides that undergo fast hydrolysis under mild conditions are valuable sources of information about how amide bonds may be activated in enzymatic transformations. We report a compound possessing an unconstrained amide bond surrounded by an amino and a carboxyl group, each mounted in close proximity on a bicyclic scaffold. Fast amide hydrolysis of this model compound was found to depend on the presence of both the amino and carboxyl functions, and to involve a proton transfer in the rate-limiting step. Possible mechanisms for the hydrolytic cleavage and their relevance to peptide bond cleavage catalyzed by natural enzymes are discussed. Experimental observations suggest that the most probable mechanisms of the model compound hydrolysis might include a twisted amide intermediate and a rate-determining proton transfer.

Ir-Catalyzed Asymmetric Total Synthesis of (-)-Communesin F.

The first catalytic asymmetric total synthesis of the heptacyclic alkaloid (-)-communesin F is described. A key step features an iridium-catalyzed asymmetric intermolecular cascade cyclization, constructing the lower N,N-aminal-containing CDEF tetracyclic core in one step. Another notable element is the closure of final ring system (A ring) via a facile reduction of a twisted amide and concomitant cyclization activated by mesylation of N,O-hemiaminal intermediate.

Structures of Highly Twisted Amides Relevant to Amide N-C Cross-Coupling: Evidence for Ground-State Amide Destabilization.

Herein, we show that acyclic amides that have recently enabled a series of elusive transition-metal-catalyzed N-C activation/cross-coupling reactions are highly twisted around the N-C(O) axis by a new destabilization mechanism of the amide bond. A unique effect of the N-glutarimide substituent, leading to uniformly high twist (ca. 90°) irrespective of the steric effect at the carbon side of the amide bond has been found. This represents the first example of a twisted amide that does not bear significant steric hindrance at the α-carbon atom. The (15) N NMR data show linear correlations between electron density at nitrogen and amide bond twist. This study strongly supports the concept of amide bond ground-state twist as a blueprint for activation of amides toward N-C bond cleavage. The new mechanism offers considerable opportunities for organic synthesis and biological processes involving non-planar amide bonds.

Facile solvolysis of a surprisingly twisted tertiary amide

A twisted 3° amide is cleaved at the same rate as a methyl ester under alkaline conditions at 22 °C.

Does hydrohalic acid HX (X = F, Cl) form true N-protonated twisted amide salts? Effects of anions on the ion-pair interactions and on the amide moiety in N-protonated tricyclic twisted amide salts

The [BF4]− and [RSO3]− anions interact with N-protonated amide cations through N–H⋯F and N–H⋯O strong hydrogen bonds and hydrohalic acids form very weak N⋯H–X hydrogen bonds.

Kinetic Isotope Effects Support the Twisted Amide Mechanism of Pin1 Peptidyl-Prolyl Isomerase

The Pin1 peptidyl-prolyl isomerase catalyzes isomerization of pSer/pThr-Pro motifs in regulating the cell cycle. Peptide substrates, Ac-Phe-Phe-phosphoSer-Pro-Arg-p-nitroaniline, were synthesized in unlabeled form, and with deuterium-labeled Ser-d3 and Pro-d7 amino acids. Kinetic data were collected as a function of Pin1 concentration to measure kinetic isotope effects (KIEs) on catalytic efficiency (kcat/Km). The normal secondary (2°) KIE value measured for the Ser-d3 substrate (kH/kD = 1.6 ± 0.2) indicates that the serine carbonyl does not rehybridize from sp(2) to sp(3) in the rate-determining step, ruling out a nucleophilic addition mechanism. The normal 2° KIE can be explained by hyperconjugation between Ser α-C-H/D and C═O and release of steric strain upon rotation of the amide bond from cis to syn-exo. The inverse 2° KIE value (kH/kD = 0.86 ± 0.08) measured for the Pro-d7 substrate indicates rehybridization of the prolyl nitrogen from sp(2) to sp(3) during the rate-limiting step of isomerization. No solvent kinetic isotope was measured by NMR exchange spectroscopy (kH2O/kD2O = 0.92 ± 0.12), indicating little or no involvement of exchangeable protons in the mechanism. These results support the formation of a simple twisted amide transition state as the mechanism for peptidyl prolyl isomerization catalyzed by Pin1. A model of the reaction mechanism is presented using crystal structures of Pin1 with ground state analogues and an inhibitor that resembles a twisted amide transition state.

A New Twist on Amide Solvolysis

Planar but destabilized: Amides prepared from hindered amines and carbonyl compounds containing an electron-withdrawing substituent (EWG) have recently been shown to undergo solvolysis at greatly enhanced rates under neutral conditions. The key is increased access to a twisted amide conformation that undergoes a proton switch, ultimately leading to the observed products.

Acid‐Catalyzed Reactions of Twisted Amides in Water Solution: Competition between Hydration and Hydrolysis

The acid-catalyzed reactions of twisted amides in water solution were investigated by using cluster-continuum model calculations. In contrast to the previous widely suggested concerted hydration of the C=O group, our calculations show that the reaction proceeds in a practically stepwise manner, and that the hydration and hydrolysis channels of the C-N bond compete. The Eigen ion (H(3)O(+)) is the key species involved in the reaction, and it modulates the hydration and hydrolysis reaction pathways. The phenyl substitution in the twisted amide not only activates the N-CO bond, but also stabilizes the hydrolysis product through n(N)→π(phenyl) delocalization, leading exclusively to the hydrolysis product of the ring-opened carboxylic acid. Generally, the twisted amides are more active than the planar amides, and such a rate acceleration results mainly from the increase in exothermicity in the first N-protonation step; the second step of the nucleophilic attack is less affected by the twisting of the amide bond. The present results show good agreement with the available experimental observations.

Proximity effects in nucleophilic addition reactions to medium-bridged twisted lactams: remarkably stable tetrahedral intermediates.

The reactions of a series of strained bicyclic and tricyclic one-carbon bridged lactams with organometallic reagents have been investigated. These amides permit isolation of a number of remarkably stable hemiaminals upon nucleophilic addition to the twisted amide bonds present in the lactam precursors. The factors that affect the stability of the resulting bridged hemiaminals are presented. In some cases, the hemiaminals were found to collapse to the open-form amino ketones in a manner expected for traditional carboxylic acid derivatives. Transannular N...C=O interactions were also observed in some nine-membered amino ketones. Additionally, tricyclic bridged lactams were found to react with some nucleophiles that typically react with ketones but not with planar amides. The effect of geometry on the reactivity of amide bonds and the amide bond distortion range that marks the boundary of amide-like and ketone-like carbonyl reactivity of lactams are also discussed.

Stability of Medium-Bridged Twisted Amides in Aqueous Solutions

"Twisted" amides containing nonstandard dihedral angles are typically hypersensitive to hydrolysis, a feature that has stringently limited their utility in water. We have synthesized a series of bridged lactams that contain a twisted amide linkage but exhibit enhanced stability in aqueous environments. Many of these compounds were extracted unchanged from aqueous mixtures ranging from the strongly basic to the strongly acidic. NMR experiments showed that tricyclic lactams undergo reversible hydrolysis at extreme pH ranges but that a number of compounds in this structure class are indefinitely stable under physiologically relevant pH conditions; one bicyclic example was additionally water-soluble. We examined the effect of structure on the reversibility of amide bond hydrolysis, which we attributed to the transannular nature of the amino acid analogs. These data suggest that medium-bridged lactams of these types should provide useful platforms for studying the behavior of twisted amides in aqueous systems.