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, as in 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.
In organic chemistry, thioesters are organosulfur compounds with the molecular structure R−C(=O)−S−R’. They are analogous to carboxylate esters with the sulfur in the thioester replacing oxygen in the carboxylate ester, as implied by the thio- prefix. They are the product of esterification of a carboxylic acid with a thiol. In biochemistry, the best-known thioesters are derivatives of coenzyme A, e.g., acetyl-CoA. The R and R' represent organyl groups, or H in the case of R.
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.
1,1'-Carbonyldiimidazole (CDI) is an organic compound with the molecular formula (C3H3N2)2CO. It is a white crystalline solid. It is often used for the coupling of amino acids for peptide synthesis and as a reagent in organic synthesis.
The Reformatsky reaction is an organic reaction which condenses aldehydes or ketones with α-halo esters using metallic zinc to form β-hydroxy-esters:
The Weinreb ketone synthesis or Weinreb–Nahm ketone synthesis is a chemical reaction used in organic chemistry to make carbon–carbon bonds. It was discovered in 1981 by Steven M. Weinreb and Steven Nahm as a method to synthesize ketones. The original reaction involved two subsequent nucleophilic acyl substitutions: the conversion of an acid chloride with N,O-Dimethylhydroxylamine, to form a Weinreb–Nahm amide, and subsequent treatment of this species with an organometallic reagent such as a Grignard reagent or organolithium reagent. Nahm and Weinreb also reported the synthesis of aldehydes by reduction of the amide with an excess of lithium aluminum hydride.
In chemistry, aminolysis (/am·i·nol·y·sis/) is any chemical reaction in which a molecule is lysed by reacting with ammonia or an amine. The case where the reaction involves ammonia may be more specifically referred to as ammonolysis.
PyBOP is a peptide coupling reagent used in solid phase peptide synthesis. It is used as a substitute for the BOP reagent - avoiding the formation of the carcinogenic waste product HMPA.
Hydroxybenzotriazole is an organic compound that is a derivative of benzotriazole. It is a white crystalline powder, which as a commercial product contains some water. Anhydrous HOBt is explosive.
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.
N,N′-Diisopropylcarbodiimide is a carbodiimide used in peptide synthesis. As a liquid, it is easier to handle than the commonly used N,N′-dicyclohexylcarbodiimide, a waxy solid. In addition, N,N′-diisopropylurea, its byproduct in many chemical reactions, is soluble in most organic solvents, a property that facilitates work-up.
HATU is a reagent used in peptide coupling chemistry to generate an active ester from a carboxylic acid. HATU is used along with Hünig's base (N,N-diisopropylethylamine), or triethylamine to form amide bonds. Typically DMF is used as solvent, although other polar aprotic solvents can also be used.
1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide is a water-soluble carbodiimide usually handled as the hydrochloride.
In organic chemistry, carbonyl reduction is the conversion of any carbonyl group, usually to an alcohol. It is a common transformation that is practiced in many ways. Ketones, aldehydes, carboxylic acids, esters, amides, and acid halides - some of the most pervasive functional groups, -comprise carbonyl compounds. Carboxylic acids, esters, and acid halides can be reduced to either aldehydes or a step further to primary alcohols, depending on the strength of the reducing agent. Aldehydes and ketones can be reduced respectively to primary and secondary alcohols. In deoxygenation, the alcohol group can be further reduced and removed altogether by replacement with H.
Retosiban also known as GSK-221,149-A is an oral drug which acts as an oxytocin receptor antagonist. It is being developed by GlaxoSmithKline for the treatment of preterm labour. Retosiban has high affinity for the oxytocin receptor and has greater than 1400-fold selectivity over the related vasopressin receptors
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.
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.
Tetramethylurea is the organic compound with the formula (Me2N)2CO. It is a substituted urea. This colorless liquid is used as an aprotic-polar solvent, especially for aromatic compounds and is used e. g. for Grignard reagents.
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.
TCFH is an electrophilic amidine reagent used to activate a number of functional groups for reaction with nucleophilies. TCFH is most commonly used to activate carboxylic acids for reaction with amines in the context of amide bond formation and peptide synthesis.
