Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Amide bond cleavage: acceleration due to a 1,3-diaxial interaction with a carboxylic acid.

ABSTRACT: To independently assess the contribution of ground-state pseudoallylic strain to the enormous rates of amide bond cleavage in tertiary amide derivatives of Kemp's triacid, we have studied four amide derivatives of (1alpha-3alpha-5beta)-5-tert-butyl-1,3-cyclohexanedicarboxylic acid. Our results demonstrate that absent pseudoallylic strain, a 1,3-diaxial interaction of an amide with a carboxylic acid leads to only a 2400-fold increase in the rate of amide bond cleavage as compared with the rate of hydrolysis of an unactivated peptide bond.

SUBMITTER: Gerschler JJ

PROVIDER: S-EPMC2518966 | biostudies-literature | 2007 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Amide bond cleavage: acceleration due to a 1,3-diaxial interaction with a carboxylic acid.

Gerschler Jared J JJ Wier Kevin A KA Hansen David E DE

The Journal of organic chemistry 20070101 2

To independently assess the contribution of ground-state pseudoallylic strain to the enormous rates of amide bond cleavage in tertiary amide derivatives of Kemp's triacid, we have studied four amide derivatives of (1alpha-3alpha-5beta)-5-tert-butyl-1,3-cyclohexanedicarboxylic acid. Our results demonstrate that absent pseudoallylic strain, a 1,3-diaxial interaction of an amide with a carboxylic acid leads to only a 2400-fold increase in the rate of amide bond cleavage as compared with the rate of ...[more]

PMID: 17221991

Similar Datasets

Carboxylic Acid Deoxyfluorination and One-Pot Amide Bond Formation Using Pentafluoropyridine (PFP).

Project description:This work describes the application of pentafluoropyridine (PFP), a cheap commercially available reagent, in the deoxyfluorination of carboxylic acids to acyl fluorides. The acyl fluorides can be formed from a range of acids under mild conditions. We also demonstrate that PFP can be utilized in a one-pot amide bond formation via in situ generation of acyl fluorides. This one-pot deoxyfluorination amide bond-forming reaction gives ready access to amides in yields of ≤94%.

| S-EPMC8397423 | biostudies-literature

How the glycosyltransferase OGT catalyzes amide bond cleavage.

Project description:The essential human enzyme O-linked ?-N-acetylglucosamine transferase (OGT), known for modulating the functions of nuclear and cytoplasmic proteins through serine and threonine glycosylation, was unexpectedly implicated in the proteolytic maturation of the cell cycle regulator host cell factor-1 (HCF-1). Here we show that HCF-1 cleavage occurs via glycosylation of a glutamate side chain followed by on-enzyme formation of an internal pyroglutamate, which undergoes spontaneous backbone hydrolysis.

| S-EPMC5172607 | biostudies-literature

l-2-Nitrimino-1,3-diazepane-4-carboxylic acid.

Project description:The cyclic form of l-nitro-arginine, C(6)H(10)N(4)O(4), crystallizes with two independent mol-ecules in the asymmetric unit. According to the geometrical parameters, similar in both mol-ecules, the structure corresponds to that of l-2-nitrimino-1,3-diazepane-4-carboxylic acid; there are, however, conformational differences between the independent molecules, one of them being close to a twisted chair while the other might be described as a rather flattened boat. All six active H atoms in the two molecules are involved in hydrogen bonds, two of which are intra-molecular and four inter-molecular, forming an infinite chain of mol-ecules along the b axis.

| S-EPMC2961324 | biostudies-literature

Instability of Amide Bond with Trifluoroacetic Acid (20%): Synthesis, Conformational Analysis, and Mechanistic Insights into Cleavable Amide Bond Comprising β-Troponylhydrazino Acid.

Project description:The instability of an amide bond with dilute trifluoroacetic acid (TFA) is a rare chemical event. The native amide bonds are stable even in the neat TFA, which is one of the reagents that releases the peptides from the solid support in the solid-supported peptide synthesis method. In the repertoire of unnatural peptidomics, α-/β-hydrazino acids and their peptides are explored for the synthesis of N-amino peptide derivatives, and their amide bonds are stable in TFA (∼100%) as natural amide bonds. This report describes the synthesis of a β-hydrazino acid analogue as β-troponylhydrazino acid, containing a nonbenzenoid natural troponyl scaffold. The structural and conformational studies of their hybrid di-/tripeptides with the natural amino acid show that the 2-aminotroponyl residue is involved in hydrogen bonding. Surprisingly, the amide bond of β-troponylhydrazino peptides is cleavable with TFA (∼20%) through the formation of a new heterocyclic molecule N-troponylpyrazolidinone or troponylpyrazolidinone. Tropolone and related compounds are excellent biocompatible chromophores. Hence, β-troponylhydrazino acid could be employed for tuning the peptide structure and considered a promising chromophoric acid-sensitive protecting group of a free amine of amino acids/peptides. It could be applied for the estimation of the free amine group functionality by a UV-vis spectrophotometer.

| S-EPMC7557997 | biostudies-literature

Efficient amide bond formation through a rapid and strong activation of carboxylic acids in a microflow reactor.

Project description:The development of highly efficient amide bond forming methods which are devoid of side reactions, including epimerization, is important, and such a method is described herein and is based on the concept of rapid and strong activation of carboxylic acids. Various carboxylic acids are rapidly (0.5 s) converted into highly active species, derived from the inexpensive and less-toxic solid triphosgene, and then rapidly (4.3 s) reacted with various amines to afford the desired peptides in high yields (74%-quant.) without significant epimerization (?3%). Our process can be carried out at ambient temperature, and only CO2 and HCl salts of diisopropylethyl amine are generated. In the long history of peptide synthesis, a significant number of active coupling reagents have been abandoned because the highly active electrophilic species generated are usually susceptible to side reactions such as epimerization. The concept presented herein should renew interest in the use of these reagents.

| S-EPMC4499250 | biostudies-literature

A Proline Mimetic for the Design of New Stable Secondary Structures: Solvent-Dependent Amide Bond Isomerization of (<i>S</i>)-Indoline-2-carboxylic Acid Derivatives.

Project description:A thorough experimental and computational study on the conformational properties of (S)-indoline-2-carboxylic acid derivatives has been conducted. Methyl (S)-1-acetylindoline-2-carboxylate, both a mimetic of proline and phenylalanine, shows a remarkable tendency toward the cis amide isomer when dissolved in polar solvents. This behavior is opposite to the general preference of proline for the trans isomer, making indoline-2-carboxylic acid a good candidate for the design of different secondary structures and new materials.

| S-EPMC8456495 | biostudies-literature

trans-4-(1-Naphth-yl)-2-oxo-1,3-oxazolidine-5-carboxylic acid.

Project description:The crystal structure of the title compound, C(14)H(11)NO(4), is influenced by N-H?O and O-H?O hydrogen bonds, linking mol-ecules into one-dimensional tapes running along the [010] direction.

| S-EPMC2962114 | biostudies-literature

2-(2-Chloro-phen-yl)-5-methyl-1,3-dioxane-5-carboxylic acid.

Project description:In the title compound, C(12)H(13)ClO(4), the 1,3-dioxane ring adopts a chair conformation and the 2-chloro-benzene and methyl substituents occupy equatorial sites. The carboxyl group is in an axial inclination. In the crystal, carb-oxy-lic acid inversion dimers linked by pairs of O-H?O hydrogen bonds generate R(2) (2)(8) loops.

| S-EPMC3393306 | biostudies-literature

A Single Enzyme Transforms a Carboxylic Acid into a Nitrile through an Amide Intermediate.

Project description:The biosynthesis of nitriles is known to occur through specialized pathways involving multiple enzymes; however, in bacterial and archeal biosynthesis of 7-deazapurines, a single enzyme, ToyM, catalyzes the conversion of the carboxylic acid containing 7-carboxy-7-deazaguanine (CDG) into its corresponding nitrile, 7-cyano-7-deazaguanine (preQ0 ). The mechanism of this unusual direct transformation was shown to proceed via the adenylation of CDG, which activates it to form the newly discovered amide intermediate 7-amido-7-deazaguanine (ADG). This is subsequently dehydrated to form the nitrile in a process that consumes a second equivalent of ATP. The authentic amide intermediate is shown to be chemically and kinetically competent. The ability of ToyM to activate two different substrates, an acid and an amide, accounts for this unprecedented one-enzyme catalysis of nitrile synthesis, and the differential rates of these two half reactions suggest that this catalytic ability is derived from an amide synthetase that gained a new function.

| S-EPMC4767005 | biostudies-literature

Facile cleavage of C-C bond: conversion of pyrane derivative to 1,3-oxazin derivative.

Project description:A cascade reaction that involves a unique C-C bond cleavage has been discovered. This protocol affords an unusual and facile method for the synthesis of 1,3-oxazin derivatives under mild conditions.

| S-EPMC7111841 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data