Effects of C(O)−N Bond Rotation on the 13C, 15N, and 17O NMR Chemical Shifts, and Infrared Carbonyl Absorption in a Series of Twisted Amides

N- to C-Peptide Synthesis, Arguably the Future for Sustainable Production

A revolution in peptide production arrived from the innovation of carboxylate to amine C- to N-direction solid-phase synthesis. This cornerstone of modern peptide science has enabled multiple academic and industrial applications; however, the process of C- to N-solid phase peptide synthesis (C-N-SPPS) has extreme process mass intensity and poor atom economy. Notably, C-N-SPPS relies upon the use of atom-intensive protecting groups, such as the fluorenylmethyloxycarbonyl (Fmoc) protection and wasteful excess of protected amino acids and coupling agents. On the other hand, peptide synthesis in the amine to carboxylate N- to C-direction offers potential to minimize protection and may arguably enable more efficient means for manufacturing peptides. For example, efficient amide bond formation in the N- to C-direction has been accomplished using methods employing thioesters, vinyl esters, and transamidation to achieve peptide synthesis with minimal epimerization. This review aims to provide an overview of N- to C-peptide synthesis indicating advantages in taking this avenue for sustainable peptide production.

Hydrogen Bond-Mediated Transition Metal-Free Alcoholysis of Primary Amides to Access Esters

An efficient hydrogen bond-mediated alcoholysis of primary amides was disclosed using diethyl phosphonate (DEP) as a catalyst. In this process, a wide range of primary amides and alcohols were tested and smoothly transformed to corresponding esters in moderate to good yields. This novel strategy features transition metal-free, broad substrate scope and a hydrogen bond-mediated one-pot pathway. In addition, the reaction showed a highly chemoselective o/alcoholic o-acylation of mercapto/phenolic alcohols.

19F NMR enantiodiscrimination and diastereomeric purity determination of amino acids, dipeptides, and amines

Chiral amino-group compounds are of significance for human health, such as biogenic amino acids (AAs), dipeptides, and even various drugs. Enantiospecific discrimination of these chiral compounds is vital in diagnosing diseases, identifying pathological biomarkers and enhancing pharmaceutical chemistry research. Here, we report a simple and rapid 19F NMR-based strategy to differentiate chiral AAs, dipeptides, and amines, that were derivatized with (R)-2-(2-fluorophenyl)-2-hydroxyacetic acid ((R)-2FHA). As a result, 19 proteinogenic AAs (37 isomers) as well as Gly could be concurrently resolved. Moreover, various mirror-image dipeptides, such as Ser-His, Leu-Leu, and Ala-Ala, were commendably recognized. Intriguingly, we found that the absolute configuration of AAs in the N-terminus of dipeptides decided the relative 19F chemical shifts between two enantiomers. Besides, the ability of this method for enantiodiscrimination was further demonstrated by non-AA amines, including aromatic and aliphatic amines, and even amines having chiral centers several carbons away from the amino-group. The structurally similar antibiotics, amoxicillin and ampicillin, were well discriminated. Furthermore, this method accurately determines the de or dr values of non-racemic mixtures. Therefore, our strategy provides an effective approach for 19F NMR-based enantiodiscrimination and diastereomeric purity determination of amino-group compounds.

Acyclic Twisted Amides

In this contribution, we provide a comprehensive overview of acyclic twisted amides, covering the literature since 1993 (the year of the first recognized report on acyclic twisted amides) through June 2020. The review focuses on classes of acyclic twisted amides and their key structural properties, such as amide bond twist and nitrogen pyramidalization, which are primarily responsible for disrupting nN to π*C═O conjugation. Through discussing acyclic twisted amides in comparison with the classic bridged lactams and conformationally restricted cyclic fused amides, the reader is provided with an overview of amidic distortion that results in novel conformational features of acyclic amides that can be exploited in various fields of chemistry ranging from organic synthesis and polymers to biochemistry and structural chemistry and the current position of acyclic twisted amides in modern chemistry.

Electrophilicity Scale of Activated Amides: 17 O NMR and 15 N NMR Chemical Shifts of Acyclic Twisted Amides in N-C(O) Cross-Coupling

The structure and properties of amides are of tremendous interest in organic synthesis and biochemistry. Traditional amides are planar and the carbonyl group non-electrophilic due to n_N →π*_C=O conjugation. In this study, we report electrophilicity scale by exploiting ¹⁷ O NMR and ¹⁵ N NMR chemical shifts of acyclic twisted and destabilized acyclic amides that have recently received major attention as precursors in N-C(O) cross-coupling by selective oxidative addition as well as precursors in electrophilic activation of N-C(O) bonds. Most crucially, we demonstrate that acyclic twisted amides feature electrophilicity of the carbonyl group that ranges between that of acid anhydrides and acid chlorides. Furthermore, a wide range of electrophilic amides is possible with gradually varying carbonyl electrophilicity by steric and electronic tuning of amide bond properties. Overall, the study quantifies for the first time that steric and electronic destabilization of the amide bond in common acyclic amides renders the amide bond as electrophilic as acid anhydrides and chlorides. These findings should have major implications on the fundamental properties of amide bonds.

Catalytic Cleavage of Amide C-N Bond: Scandium, Manganese, and Zinc Catalysts for Esterification of Amides

Amide C-N bonds are thermodynamically stable and their fission, such as by hydrolysis and alcoholysis, is considered a long-challenging organic reaction. In general, stoichiometric chemical transformations of amides into the corresponding esters and acids require harsh conditions, such as strong acids/bases at a high reaction temperature. Accordingly, the development of catalytic reactions that cleave not only primary and secondary amides, but also tertiary amides in mild conditions, is in high demand. Herein, we surveyed typical stoichiometric transformations of amides, and highlight our recent achievements in the catalytic esterification of amides using scandium, manganese, and zinc catalysts, together with some recent catalyst systems using late-transition metal reported by other groups.

17O NMR and 15N NMR chemical shifts of sterically-hindered amides: ground-state destabilization in amide electrophilicity

The structure and spectroscopic properties of the amide bond are a topic of fundamental interest in chemistry and biology. Herein, we report 17O NMR and 15N NMR spectroscopic data for four series of sterically-hindered acyclic amides. Despite the utility of 17O NMR and 15N NMR spectroscopy, these methods are severely underutilized in the experimental determination of electronic properties of the amide bond. The data demonstrate that a combined use of 17O NMR and 15N NMR serves as a powerful tool in assessing electronic effects of the amide bond substitution as a measure of electrophilicity of the amide bond. Notably, we demonstrate that steric destabilization of the amide bond results in electronically-activated amides that are comparable in terms of electrophilicity to acyl fluorides and carboxylic acid anhydrides.

Twisting the ethano-Tröger's base: the bisamide

The typically planar amide when incorporated into bicyclic systems can undergo a significant distortion from planarity resulting in physical properties and reactivity that deviate from classical amide behaviour. Herein, we report a succinct protocol that utilises potassium permanganate to selectively α-oxygenate the benzylic position of ethano-Tröger's base derivatives to yield a new class of twisted bisamides. Additionally, we report the first synthesis of an ethano-Tröger's base derivative bearing substituents in the positions ortho to the nitrogen atoms.

Fe-catalyzed esterification of amides via C–N bond activation

An efficient Fe-catalyzed esterification of primary, secondary, and tertiary amides with various alcohols was performed. Esterification was accomplished with inexpensive, environmentally friendly FeCl₃·6H₂O, and with high functional group tolerance

Structural Basis of Protein Asn-Glycosylation by Oligosaccharyltransferases

Glycosylation of asparagine residues is a ubiquitous protein modification. This N-glycosylation is essential in Eukaryotes, but principally nonessential in Prokaryotes (Archaea and Eubacteria), although it facilitates their survival and pathogenicity. In many reviews, Archaea have received far less attention than Eubacteria, but this review will cover the N-glycosylation in the three domains of life. The oligosaccharide chain is preassembled on a lipid-phospho carrier to form a donor substrate, lipid-linked oligosaccharide (LLO). The en bloc transfer of an oligosaccharide from LLO to selected Asn residues in the Asn-X-Ser/Thr (X≠Pro) sequons in a polypeptide chain is catalyzed by a membrane-bound enzyme, oligosaccharyltransferase (OST). Over the last 10 years, the three-dimensional structures of the catalytic subunits of the Stt3/AglB/PglB proteins, with an acceptor peptide and a donor LLO, have been determined by X-ray crystallography, and recently the complex structures with other subunits have been determined by cryo-electron microscopy . Structural comparisons within the same species and across the different domains of life yielded a unified view of the structures and functions of OSTs. A catalytic structure in the TM region accounts for the amide bond twisting, which increases the reactivity of the side-chain nitrogen atom of the acceptor Asn residue in the sequon. The Ser/Thr-binding pocket in the C-terminal domain explains the requirement for hydroxy amino acid residues in the sequon. As expected, the two functional structures are formed by the involvement of short amino acid motifs conserved across the three domains of life.

An efficient computational model to predict protonation at the amide nitrogen and reactivity along the C-N rotational pathway

N-Protonation of amides is critical in numerous biological processes, including amide bonds proteolysis and protein folding as well as in organic synthesis as a method to activate amide bonds towards unconventional reactivity. A computational model enabling prediction of protonation at the amide bond nitrogen atom along the C-N rotational pathway is reported. Notably, this study provides a blueprint for the rational design and application of amides with a controlled degree of rotation in synthetic chemistry and biology.

Are the amide bonds in N-acyl imidazoles twisted? A combined solid-state 17O NMR, crystallographic, and computational study

We report synthesis of 17O-labeling and solid-state 17O NMR measurements of three N-acyl imidazoles of the type R-C(17O)-Im: R = p-methoxycinnamoyl (MCA-Im), R = 4-(dimethylamino)benzoyl (DAB-Im), and R = 2,4,6-trimethylbenzoyl (TMB-Im). Solid-state 17O NMR experiments allowed us to determine for the first time the 17O quadrupole coupling and chemical shift tensors in this class of organic compounds. We also determined the crystal structures of these compounds using single-crystal X-ray diffraction. The crystal structures show that, while the C(O)–N amide bond in DAB-Im exhibits a small twist, those in MCA-Im and TMB-Im are essentially planar. We found that, in these N-acyl imidazoles, the 17O quadrupole coupling and chemical shift tensors depend critically on the torsion angle between the conjugated acyl group and the C(O)–N amide plane. The computational results from a plane-wave DFT approach, which takes into consideration the entire crystal lattice, are in excellent agreement with the experimental solid-state 17O NMR results. Quantum chemical computations also show that the dependence of 17O NMR parameters on the Ar–C(O) bond rotation is very similar to that previously observed for the C(O)–N bond rotation in twisted amides. We conclude that one should be cautious in linking the observed NMR chemical shifts only to the twist of the C(O)–N amide bond.

Peptide bond distortions from planarity: new insights from quantum mechanical calculations and peptide/protein crystal structures

By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of C(α) substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed.

Reactive intermediates in peptide synthesis. Molecular and crystal structures of reactive carboxylic amides

The molecular and crystal structures of N-para-toluenesulphonyl-N-methyl-α-aminoisobutyric acyl imidazole (1), and 3-(N-para-toluenesulphonyl-α-aminoisobutyric acyl)-1,3-thiazolidine-2-thione (2) have been determined by X-ray diffraction. Crystal parameters: (1) orthorhombic, space group P212121, a = 11.735(2) Å, b = 19.990(3) Å, c = 6.925(1) Å, and Z = 4; (2) orthorhombic, space group Pnc2, a = 9.507(2) Å, b = 16.902(2) Å, c = 10.347(2) Å, and Z = 4. The structures were solved by direct methods. The least-squares refinements led to conventional R factors of 0.036 and 0.031 for (1) and (2), respectively. This is the first geometrical and conformational characterization at atomic resolution of N α -protected α-aminoacids containing the elusive acyl imidazole and 3-acyl-1,3-thiazolidine-2-thione C-activating groups. Only the reactive carboxylic amide of (2) deviates significantly from planarity.

Resonance structures of the amide bond: the advantages of planarity

Delocalization indexes based on magnitudes derived from electron-pair densities are demonstrated to be useful indicators of electron resonance in amides. These indexes, based on the integration of the two-electron density matrix over the atomic basins defined through the zero-flux condition, have been calculated for a series of amides at the B3LYP/6-31+G* level of theory. These quantities, which can be viewed as a measure of the sharing of electrons between atoms, behave in concordance with the traditional resonance model, even though they are integrated in Bader atomic basins. Thus, the use of these quantities overcomes contradictory results from analyses of atomic charges, yet keeps the theoretical appeal of using nonarbitrary atomic partitions and unambiguously defined functions such as densities and pair densities. Moreover, for a large data set consisting of 24 amides plus their corresponding rotational transition states, a linear relation was found between the rotational barrier for the amide and the delocalization index between the nitrogen and oxygen atoms, indicating that this parameter can be used as an ideal physical-chemical indicator of the electron resonance in amides.

“Amide Resonance” Correlates with a Breadth of C−N Rotation Barriers

Complete basis set calculations (CBS-QB3) were used to compute the CN rotation barriers for acetamide and eight related compounds, including acetamide enolate and O-protonated acetamide. Natural resonance theory analysis was employed to quantify the "amide resonance" contribution to ground-state electronic structures. A range of rotation barriers, spanning nearly 50 kcal/mol, correlates well to the ground-state resonance weights without the need to account for transition-state effects. Use of appropriate model compounds is crucial to gain an understanding of the structural and electronic changes taking place during rotation of the CN bond in acetamide. The disparate changes in bond length (DeltarCO << DeltarCN) are found to be consonant with the resonance model. Similarly, charge differences are consistent with donation from the nitrogen lone pair electrons into the carbonyl pi* orbital. Despite recent attacks on the resonance model, these findings demonstrate it to be a sophisticated and highly predictive tool in the chemist's arsenal.

The chemistry of nitrogen coordinated tertiary carboxamides: a spectroscopic study on bis(picolyl)amidecopper(ii) complexes

Metal coordination of the electrically neutral nitrogen atom of a tertiary carboxamide reduces the barrier to C-N-bond rotation and activates the amide towards methanolysis. X-Ray crystallographic studies indicate that this reactivity is correlated to a lifting of the amide resonance structure and concurrent pyramidalization at nitrogen. However, mechanistic data in solution have not been obtained. It became evident that structural mobility is characteristic of the complexes and the crystallographic data do not fully account for relevant reactive species. In this report we summarize IR, UV-vis, and EPR spectra of amide nitrogen coordinated bis(picolyl)amide complexes with copper(II) triflate and copper(II) chloride. A comparison between spectra sampled in the aprotic solvents dichloromethane and acetonitrile, as well as under methanolysis conditions reveals the nature of several species formed in solution. The key reactions are (I) ligand exchange involving either CH3CN or CH3OH, or, in IR experiments, bromide ions from KBr, (II) coordination-dissociation equilibria involving the urethane protecting groups of amino acid substituted ligands Boc-Xaa-bpa (Boc = tert-butoxycarbonyl, Xaa = glycine, alanine, and leucine, respectively, bpa = bis(picolyl)amine), (III) dissociation of a chloro ligand from LCuCl2 complexes and formation of square-pyramidal complex cations [LCuCl]+, and finally (IV) complete dissociation of the polydentate tertiary amide ligand to produce free copper ions in solution. Taken together, the results provide a fairly detailed qualitative picture of the processes which accompany the amide bond methanolysis.

Semisynthesis of a segmental isotopically labeled protein splicing precursor: NMR evidence for an unusual peptide bond at the N-extein-intein junction

Protein splicing is a posttranslational autocatalytic process in which an intervening sequence, termed an intein, is removed from a host protein, the extein. Although we have a reasonable picture of the basic chemical steps in protein splicing, our knowledge of how these are catalyzed and regulated is less well developed. In the current study, a combination of NMR spectroscopy and segmental isotopic labeling has been used to study the structure of an active protein splicing precursor, corresponding to an N-extein fusion of the Mxe GyrA intein. The (1)J(NC') coupling constant for the (-1) scissile peptide bond at the N-extein-intein junction was found to be approximately 12 Hz, which indicates that this amide is highly polarized, perhaps because of nonplanarity. Additional mutagenesis and NMR studies indicate that conserved box B histidine residue is essential for catalysis of the first step of splicing and for maintaining the (-1) scissile bond in its unusual conformation. Overall, these studies support the "ground-state destabilization" model as part of the mechanism of catalysis.

H-bonding mediates polarization of peptide groups in folded proteins

The carbon-nitrogen J-couplings in the hydrogen bonding chains of proteins show that H-bonding mediates peptide-group polarization, which results in the general reduction of peptide-group polarity of folded proteins in solution. The net effect is to make large regions of protein secondary structure, especially beta-sheets, intrinsically more hydrophobic, contributing thereby to overall stability of the tertiary structure.

N-substituent effect on the cis-trans geometry of nine-membered lactams

The cis-trans geometry of a nine-membered lactam significantly depends on the N-substituents; N-acyl-1-aza-2-cyclononanones (1a-c) exist as cis form; in contrast, N-Z- 1-aza-2-cyclononanone (1d) exists as trans form both in the crystal and in solution.

[Nitrogen pyramidal amides and related compounds]

A planar amide bond is a fundamental linkage in the structures of peptides and proteins. The rigid planarity of the amide linkage, due to a conjugation between carbonyl and amine groups, may be requisite for encoded protein folding and many other biological processes. Non-planar amides in the ground state will decode the significance of the planarity and rigidity of the amide linkage. We show here that simple amides of 7-azabicyclo[2.2.1]heptane, free from steric bias, including parent N-benzoyl 7-azabicyclo[2.2.1]heptane, are nitrogen-pyramidal amides in the crystalline state. We can suggest that pyramidalized amide nitrogen is a general feature and intrinsic to the 7-azabicyclo[2.2.1]heptane motif. Low rotational barriers of the amide C-N bond in a series of N-benzoyl amides of 7-azabicyclo[2.2.1]heptane, compared to monocyclic amides, may imply that ground-state nitrogen pyramidalization of the former amides also exist in solution. The 7-azabicyclo[2.2.1]heptane motif also favors nitrogen pyramidalization of sulfonamides and N-nitrosoamines, which can lead to pharmacophores after appropriate modification.