The Nomenclature of Amides

We observed that cyclic esters (lactones) may be formed when the carboxyl electrophile and hydroxyl nucleophile are in the same molecule (see Section 7.9.1). Similarly, cyclic amides are produced when carboxyl and amine groups are in the same molecule, and are again most favoured when this results in the generation of strain-free five- or six-membered rings. Cyclic esters are termed lactones, whereas cyclic amides are in turn called lactams. The nomenclature of lactams is similar... 

Substrate specificity. Like most other enzymes, proteases display distinct preferences for certain substrates. These are often discussed using the nomenclature of Fig. 12-14. The substrate residue contributing the carbonyl of the amide group to be cleaved is designated Pj and residues toward the N terminus as P2, P3, etc., as is shown in Fig. 12-14. Residues toward the C terminus from the peptide linkage to be cleaved are designated P P etc. Chymotrypsin acts... 

The subject of glycosylamines has already been reviewed in this Series,80 and the nomenclature of these compounds, formerly called JV-glycosides, amides, anilides, etc., was discussed. 

Z/E isomerism is not limited to true double bonds and may be used when sp2 electrons of a heteroatom are conjugated with a 7r-system to form a planar pseudo double bond. In particular, in the case of amides, the cis isomer is called E. Although the general tendency now is to use the E/Z nomenclature in chemistry, despite their inaccuracy cis and trans are still utilized by biochemists because they give a more readily understandable description of molecular shape, in particular for amides in peptides and proteins. When the chains are connected through a motif containing more than three dihedral angles (i.e. carbamates), the syn-anti... 

The nomenclature of step-reaction polymers is even more complicated than that of vinyl polymers and can be quite confusing. These polymers are usually named according to the source or initial monomer(s) and the type of reaction involved in the synthesis. For example, nylon 6,6 (4) is usually designated poly(hexamethylene adipamide), indicating an amidation reaction between hexamethylene-diamine and adipic acid. Nylon 6 is called either poly(6-hexanoamide) or poly(e-caprolactam). The former name indicates the structural and derivative method while the latter, which is more commonly used, is based on the source of the monomer. 

As lactones are cyclic esters, so lactams are cyclic amides. Again, as was the case with lactones, the nomenclature of the lactams is based on the use of Greek letters to show ring size, substitution of nitrogen for carbon in a cyclic array (thus using the prefix azacyclo ), or the Hantzsch-Widman system (vide supra). Some examples follow in Table 5.14. 

The nomenclature (qv) of polyamides is fraught with a variety of systematic, semisystematic, and common naming systems used variously by different sources. In North America the common practice is to call type AB or type AABB polyamides nylon-x or nylon-respectively, where x refers to the number of carbon atoms between the amide nitrogens. For type AABB polyamides, the number of carbon atoms in the diamine is indicated first, followed by the number of carbon atoms in the diacid. For example, the polyamide formed from 6-aminohexanoic acid [60-32-2] is named nylon-6 [25038-54-4], that formed from 1,6-hexanediamine [124-09-4] or hexamethylenediamine and dodecanedioic acid [693-23-2] is called nylon-6,12 [24936-74-1]. In Europe, the common practice is to use the designation "polyamide," often abbreviated PA, instead of "nylon" in the name. Thus, the two examples above become PA-6 and PA-6,12, respectively. PA is the International Union of Pure and AppHed Chemistry (lUPAC) accepted abbreviation for polyamides. 

Because the rules for organic nomenclature determine the priority of naming different carbon chains from their relative lengths, the systematic names for type AABB polyamides depend on the relative length of the carbon chains between the amide nitrogens and the two carbonyl functions of the polymer for aUphatic nylon-Ayy, when x < the lUPAC name is poly[imino-R imino(l2y-dioxo-R )]. When x > then the name is... 

Tervalent organophosphorus compounds containing one single P-N bond with the valency of each atom saturated by protons or carbons (but no other heteroatoms) have been known since their discovery by MichaeUs more than one century ago [ 1 ] and named indistinctly as aminophosphanes, phosphanamines, phosphazanes, or phosphinous amides. This last chemical nomenclature is the one used by the Chemical Abstracts Service (CAS) for indexing these compounds and is also the one that best delimits the scope of this review those species derived from the parent H2P-NH2 (phosphinous amide in CAS nomenclature) by partial or total substitution of protons by hydrocarbon radicals (Table 1). 

Base hydrolysis of amides also requires quite vigorous conditions, but mechanistically it is exactly equivalent to base hydrolysis of esters. After nucleophilic attack of hydroxide on to the carbonyl, the tetrahedral anionic intermediate is able to lose either an amide anion (care with nomenclature here, the amide anion is quite different from the amide molecule) or hydroxide. Although loss of hydroxide is preferred, since the amide anion is a stronger base than hydroxide, this would merely reverse the reaction. 

In Chapter 9 you see the basic structure of each of the carboxylic acids and Ccirboxylic acid derivatives. In this chapter we focus on the carboxylic acids and related compounds, such as esters, acyl chlorides, and acid anhydrides, and we also include some information on amides (see Chapter 13 for an additional examination of cimides). Before you can get into synthesis and reactions, though, you need to understand the structure and nomenclature of these compounds. 

Due to the good nucleophilic nature of sulfur, formation of new C—S bonds is relatively easy. This property has been used for intramolecular peptide cyclization 1 and was exploited for preparation of methylenethio ether surrogates, t >[CH2—S], initially as peptide gap inhibitors for blocking collagenase action. 2 These surrogates were later converted into sulfoxide and sulfone derivatives. This expansion of amide replacements compelled a more generalized nomenclature system for pseudopeptides (amides with one or more amide bond surrogates) and led directly to the psi-bracket convention. 1 ... 

Secondary and tertiary amines, which have two and three substituents on nitrogen, commonly are named as N-substituted amines. As for substituted amides, N is included to indicate that the substituent is on the nitrogen atom unless there is no ambiguity as to where the substituent is located. Systematic nomenclature of secondary and tertiary amines is related to the systematic ether nomenclature discussed in Section 7-3 ... 

Replacement nomenclature emphasizes the length of the repeat unit but masks the functionality (i.e., amide) in these units. Alternatively, a repeat unit name (such as, (propanamido)methylidyne), which indicates the functionality but obscures the chain length, may be preferred. The style chosen for the internal (or core or terminal) unit name(s) does not affect the general form of the proposed cascade nomenclature. Thus, the cascade in Figure 3.5 is 36-Cascade tricyclo[3.3.l.l3,7]decane[4-l,3,5,7] (3-oxo-2-aza-propylidyne) (3-oxo-2-azapentylidyne) propanoic acid. 

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