In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula RC(=O)NR′R″, where R, R', and R″ represent organic groups or hydrogen atoms. The amide group is called a peptide bond when it is part of the main chain of a protein, and 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 RC(=O)OH with the hydroxyl group –OH replaced by an amine group –NR′R″; or, equivalently, an acyl (alkanoyl) group RC(=O)– joined to an amine group.
Combinatorial chemistry comprises chemical synthetic methods that make it possible to prepare a large number of compounds in a single process. These compound libraries can be made as mixtures, sets of individual compounds or chemical structures generated by computer software. Combinatorial chemistry can be used for the synthesis of small molecules and for peptides.
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.
The Corey–House synthesis (also called the Corey–Posner–Whitesides–House reaction and other permutations) is an organic reaction that involves the reaction of a lithium diorganylcuprate (R2CuLi) with an organyl (pseudo)halide (R'X) to form a new alkane, as well as an ill-defined organocopper species and lithium halide as byproducts.
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.
In chemistry, a polyyne is any organic compound with alternating single and triple bonds; that is, a series of consecutive alkynes, (−C≡C−)
n with n greater than 1. The simplest example is diacetylene or butadiyne, H−C≡C−C≡C−H.
Organozinc compounds in organic chemistry contain carbon to zinc chemical bonds. Organozinc chemistry is the science of organozinc compounds describing their physical properties, synthesis and reactions.
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.
Organocopper compounds in organometallic chemistry contain carbon to copper chemical bonds. Organocopper chemistry is the science of organocopper compounds describing their physical properties, synthesis and reactions. They are reagents in organic chemistry.
The Wurtz–Fittig reaction is the chemical reaction of aryl halides with alkyl halides and sodium metal in the presence of dry ether to give substituted aromatic compounds. Charles Adolphe Wurtz reported what is now known as the Wurtz reaction in 1855, involving the formation of a new carbon-carbon bond by coupling two alkyl halides. Work by Wilhelm Rudolph Fittig in the 1860s extended the approach to the coupling of an alkyl halide with an aryl halide. This modification of the Wurtz reaction is considered a separate process and is named for both scientists.
N-Hydroxysuccinimide (NHS) is an organic compound with the formula (CH2CO)2NOH. It is a white solid that is used as a reagent for preparing active esters in peptide synthesis. It can be synthesized by heating succinic anhydride with hydroxylamine or hydroxylamine hydrochloride.
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.
The Steglich esterification is a variation of an esterfication with dicyclohexylcarbodiimide as a coupling reagent and 4-dimethylaminopyridine as a catalyst. The reaction was first described by Wolfgang Steglich in 1978. It is an adaptation of an older method for the formation of amides by means of DCC (dicyclohexylcarbodiimide) and 1-hydroxybenzotriazole (HOBT).
2-Methyl-6-nitrobenzoic anhydride is an organic acid anhydride also known as the Shiina reagent, having a structure wherein carboxylic acids undergo intermolecular dehydration condensation. It was developed in 2002 by Prof. Isamu Shiina. The compound is often abbreviated MNBA.
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.
A stannatrane is a tin-based atrane belonging to the larger class of organostannanes. Though the term stannatrane is often used to refer to the more commonly employed carbastannatrane, azastannatranes have also been synthesized. Stannatrane reagents offer highly selective methods for the incorporation of "R" substituents in complex molecules for late-stage diversification. These reagents differ from their tetraalkyl organostannane analogues in that there is no participation of dummy ligands in the transmetalation step, offering selective alkyl transfer in Stille Coupling reactions. These transmetalating agents are known to be air- and moisture-stable, as well as generally less toxic than their tetraalkyl counterparts.
Organoniobium chemistry is the chemistry of compounds containing niobium-carbon (Nb-C) bonds. Compared to the other group 5 transition metal organometallics, the chemistry of organoniobium compounds most closely resembles that of organotantalum compounds. Organoniobium compounds of oxidation states +5, +4, +3, +2, +1, 0, -1, and -3 have been prepared, with the +5 oxidation state being the most common.
1,1'-Thiocarbonyldiimidazole (TCDI) is a thiourea containing two imidazole rings. It is the sulfur analog of the peptide coupling reagent carbonyldiimidazole (CDI).
