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.
A carboxylic acid is an organic acid that contains a carboxyl group attached to an R-group. The general formula of a carboxylic acid is R–COOH, with R referring to the alkyl, alkenyl, aryl, or other group. Carboxylic acids occur widely. Important examples include the amino acids and fatty acids. Deprotonation of a carboxylic acid gives a carboxylate anion.
In chemistry, an ester is a chemical compound derived from an acid in which at least one –OH (hydroxyl) group is replaced by an –O–alkyl (alkoxy) group. Usually, esters are derived from substitution reaction of a carboxylic acid and an alcohol. Glycerides, which are fatty acid esters of glycerol, are important esters in biology, being one of the main classes of lipids, and making up the bulk of animal fats and vegetable oils. Esters with low molecular weight are commonly used as fragrances and found in essential oils and pheromones. Phosphoesters form the backbone of DNA molecules. Nitrate esters, such as nitroglycerin, are known for their explosive properties, while polyesters are important plastics, with monomers linked by ester moieties. Esters usually have a sweet smell and are considered high-quality solvents for a broad array of plastics, plasticizers, resins, and lacquers. They are also one of the largest classes of synthetic lubricants on the commercial market.
In organic chemistry, an acyl chloride (or acid chloride) is an organic compound with the functional group -COCl. Their formula is usually written RCOCl, where R is a side chain. They are reactive derivatives of carboxylic acids. A specific example of an acyl chloride is acetyl chloride, CH3COCl. Acyl chlorides are the most important subset of acyl halides.
In organic chemistry, nitration is a general class of chemical processes for the introduction of a nitro group into an organic compound. The term also is applied incorrectly to the different process of forming nitrate esters between alcohols and nitric acid. The difference between the resulting molecular structures of nitro compounds and nitrates is that the nitrogen atom in nitro compounds is directly bonded to a non-oxygen atom, whereas in nitrate esters, the nitrogen is bonded to an oxygen atom that in turn usually is bonded to a carbon atom.
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.
Thionyl chloride is an inorganic compound with the chemical formula SOCl
2. It is a moderately volatile colourless liquid with an unpleasant acrid odour. Thionyl chloride is primarily used as a chlorinating reagent, with approximately 45,000 tonnes per year being produced during the early 1990s. It is toxic, reacts with water, and is also listed under the Chemical Weapons Convention as it may be used for the production of chemical weapons.
Cyanuric chloride is an organic compound with the formula (NCCl)3. This white solid is the chlorinated derivative of 1,3,5-triazine. It is the trimer of cyanogen chloride. Cyanuric chloride is the main precursor to the popular but controversial herbicide atrazine.
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 organic chemistry, the Arndt–Eistert reaction is the conversion of a carboxylic acid to its homologue. Named for the German chemists Fritz Arndt (1885–1969) and Bernd Eistert (1902–1978), the method entails treating an acid chlorides with diazomethane. It is a popular method of producing β-amino acids from α-amino acids.
Aminolysis (/am·i·nol·y·sis/ amino meaning "contains NH2 group", and lysis meaning "to unbind") is any chemical reaction in which a molecule is split into two parts by reacting with ammonia or an amine..
A boronic acid is a compound related to boric acid in which one of the three hydroxyl groups is replaced by an alkyl or aryl group. As a compound containing a carbon–boron bond, members of this class thus belong to the larger class of organoboranes. Boronic acids act as Lewis acids. Their unique feature is that they are capable of forming reversible covalent complexes with sugars, amino acids, hydroxamic acids, etc.. The pKa of a boronic acid is ~9, but they can form tetrahedral boronate complexes with pKa ~7. They are occasionally used in the area of molecular recognition to bind to saccharides for fluorescent detection or selective transport of saccharides across membranes.
Diphenylketene is a chemical substance of the ketene family. Diphenylketene, like most disubstituted ketenes, is a red-orange oil at room temperature and pressure. Due to the successive double bonds in the ketene structure R1R2C=C=O, diphenyl ketene is a heterocumule. The most important reaction of diphenyl ketene is the [2+2] cycloaddition at C-C, C-N, C-O, and C-S multiple bonds.
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.
The Schotten–Baumann reaction is a method to synthesize amides from amines and acid chlorides:
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).
Trichloroacetonitrile is an organic compound with the formula CCl3CN. It is a colourless liquid, although commercial samples often are brownish. It is used commercially as a precursor to the fungicide etridiazole. It is prepared by dehydration of trichloroacetamide. As a bifunctional compound, trichloroacetonitrile can react at both the trichloromethyl and the nitrile group. The electron withdrawing effect of the trichloromethyl group activates the nitrile group for nucleophilic additions. The high reactivity makes trichloroacetonitrile a versatile reagent, but also causes its susceptibility towards hydrolysis.
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.
N-Hydroxyphthalimide is the N-hydroxy derivative of phthalimide. The compound is used, inter alia, as catalyst for oxidation reactions, in particular for the selective oxidation with molecular oxygen under mild conditions.
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.
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