In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula R−C(=O)−NR′R″, where R, R', and R″ represent any group, typically organyl groups or hydrogen atoms. The amide group is called a peptide bond when it is part of the main chain of a protein, and an isopeptide bond when it occurs in a side chain, such as in the amino acids asparagine and glutamine. It can be viewed as a derivative of a carboxylic acid with the hydroxyl group replaced by an amine group ; or, equivalently, an acyl (alkanoyl) group joined to an amine group.
The Stille reaction is a chemical reaction widely used in organic synthesis. The reaction involves the coupling of two organic groups, one of which is carried as an organotin compound. A variety of organic electrophiles provide the other coupling partner. The Stille reaction is one of many palladium-catalyzed coupling reactions.
In organic chemistry, peptide synthesis is the production of peptides, compounds where multiple amino acids are linked via amide bonds, also known as peptide bonds. Peptides are chemically synthesized by the condensation reaction of the carboxyl group of one amino acid to the amino group of another. Protecting group strategies are usually necessary to prevent undesirable side reactions with the various amino acid side chains. Chemical peptide synthesis most commonly starts at the carboxyl end of the peptide (C-terminus), and proceeds toward the amino-terminus (N-terminus). Protein biosynthesis in living organisms occurs in the opposite direction.
A lactam is a cyclic amide, formally derived from an amino alkanoic acid. The term is a portmanteau of the words lactone + amide.
Copper(I) thiophene-2-carboxylate or CuTC is a coordination complex derived from copper and thiophene-2-carboxylic acid. It is used as a reagent to promote the Ullmann reaction between aryl halides.
Sigma-Aldrich is an American chemical, life science, and biotechnology company owned by the multinational chemical conglomerate Merck Group.
BOP (benzotriazol-1-yloxytris(dimethylamino)phosphonium hexafluorophosphate) reagent is a reagent commonly used in the synthesis of peptides. Its use is discouraged because coupling using BOP liberates HMPA which is carcinogenic, although for small scale use in an organic laboratory this is not a great disadvantage as it is in large scale industrial usage. BOP has been used for peptide coupling, synthesis of esters, esterification of carboxylic acids, or as a catalyst. This reagent is advantageous in peptide coupling to other derived reagents because there are no side reactions from the dehydration of asparagine or glutamine. In peptide coupling the BOP reagent works well because it forms reactive intermediates which allow for the amines to bond together with little energy loss. In the reduction of carboxylic acids, using the BOP reagent with NaBH4 resulted in high percent yields.
Chloramine-T is the organic compound with the formula CH3C6H4SO2NClNa. Both the anhydrous salt and its trihydrate are known. Both are white powders. Chloramine-T is used as a reagent in organic synthesis. It is commonly used as cyclizing agent in the synthesis of aziridine, oxadiazole, isoxazole and pyrazoles. It's a inexpensive, low toxic and mild oxidizing agent, and it also acts as a source of nitrogen anions and electrophilic cations. But it may undergo degradation on long term exposure to atmosphere, so care must be taken during the storage.
Dimethyl pimelimidate (DMP) is an organic chemical compound with two functional imidate groups. It is usually available as the more stable dihydrochloride salt. It binds free amino groups at pH range 7.0-10.0 to form amidine bonds.
N-Ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline (EEDQ) is an irreversible dopamine-receptor antagonist.
1-Hydroxy-7-azabenzotriazole (HOAt) is a triazole used as a peptide coupling reagent. It suppresses the racemization.
1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide is a water-soluble carbodiimide usually handled as the hydrochloride. It is typically employed in the 4.0-6.0 pH range. It is generally used as a carboxyl activating agent for the coupling of primary amines to yield amide bonds. While other carbodiimides like dicyclohexylcarbodiimide (DCC) or diisopropylcarbodiimide (DIC) are also employed for this purpose, EDC has the advantage that the urea byproduct formed can be washed away from the amide product using dilute acid. Additionally, EDC can also be used to activate phosphate groups in order to form phosphomonoesters and phosphodiesters. Common uses for this carbodiimide include peptide synthesis, protein crosslinking to nucleic acids, but also in the preparation of immunoconjugates. EDC is often used in combination with N-hydroxysuccinimide (NHS) for the immobilisation of large biomolecules. Recent work has also used EDC to assess the structure state of uracil nucleobases in RNA.
Fluorescamine is a spiro compound that is not fluorescent itself, but reacts with primary amines to form highly fluorescent products, i.e. it is fluorogenic. It hence has been used as a reagent for the detection of amines and peptides. 1-100 µg of protein and down to 10 pg of protein can be detected. Once bound to protein the excitation wavelength is 381 nm and the emission wavelength is 470 nm (blue). This method is found to suffer of high blanks resulting of high rate of hydrolysis due to used excess concentration. Alternative methods are based on ortho-phthalaldehyde (OPA), Ellman's reagent (DTNB), or epicocconone.
Disuccinimidyl suberate (DSS) is a six-carbon lysine-reactive non-cleavable cross-linking agent.
PEPPSI is an abbreviation for pyridine-enhanced precatalyst preparation stabilization and initiation. It refers to a family of commercially available palladium catalysts developed around 2005 by Prof. Michael G. Organ and co-workers at York University, which can accelerate various carbon-carbon and carbon-heteroatom bond forming cross-coupling reactions. In comparison to many alternative palladium catalysts, Pd-PEPPSI-type complexes are stable to air and moisture and are relatively easy to synthesize and handle.
In organic chemistry, phosphonium coupling is a cross-coupling reaction for organic synthesis. It is a mild, efficient, chemoselective and versatile methodology for the formation of C–C, C–N, C–O, and C–S bond of unactivated and unprotected tautomerizable heterocycles. The method was originally reported in 2004. The C–OH bond of a tautomerizable heterocycle is activated with a phosphonium salt, and subsequent functionalization with either a nucleophile through SNAr displacement or an organometallic through transition metal catalyzed cross coupling reaction. The in situ activation of the C-OH bond in phosphonium coupling has been applied to cross coupling reactions of tautomerizable heterocycles and arenols using other types of activating reagents.
DEPBT is a peptide coupling reagent used in peptide synthesis. It shows remarkable resistance to racemization.
HBTU is a coupling reagent used in solid phase peptide synthesis. It was introduced in 1978 and shows resistance against racemization. It is used because of its mild activating properties.
PyAOP is a coupling reagent used in solid phase peptide synthesis. It is a derivative of the HOAt family of coupling reagents. It is preferred over HATU, because it does not side react at the N-terminus of the peptide. Compared to the HOBt derivates, PyAOP are more reactive due to the additional nitrogen.
Ethyl cyanohydroxyiminoacetate (oxyma) is the oxime of ethyl cyanoacetate and finds use as an additive for carbodiimides, such as dicyclohexylcarbodiimide (DCC) in peptide synthesis. It acts as a neutralizing reagent for the basicity or nucleophilicity of the DCC due to its pronounced acidity and suppresses base catalyzed side reactions, in particular racemization.
