Nomenclature asymmetric carbon atoms

Glucose on oxidation gives saccharic acid and on the basis of D-glucose structure, XIV would be D and XV, L on the account of the bottom asymmetric carbon atom. But if XV is rotated in the plane of paper through 180° if becomes exactly identical with XIV. Dispute like this and tartaric acid have raised great interest in improving the system of nomenclature. 

The a-carbon of all amino acids, with the exception of glycine, has four different substituent groups and is therefore an asymmetric carbon atom. Such an atom can exist in two different spatial arrangements which are mirror images of each other. These structural forms of molecules are known as stereoisomers and the common notation of D and L forms is used, a nomenclature that refers to their absolute spatial configuration when compared with that of glyceraldehyde (Figure 10.4). 

This derives from the asymmetric carbon atom at position C-2. On the basis of the nomenclature adopted in Chapter 1, this compound has an sn-3 configuration. In all the diacylphosphatidylcholine molecules found in mammalian cells and tissues, this is the only stereochemical configuration present. No evidence for the sn-2 or sn-1 configuration has been reported. 

R) and (S) Nomenclature of Asymmetric Carbon Atoms 181 5-4 Optical Activity 185... 

Identify asymmetric carbon atoms, and name them using the (A) and (S) nomenclature. 

To deal with this problem, we use the E-Z system of nomenclature (pun intended) for cis-trans isomers, which is patterned after the Cahn-Ingold-Prelog convention for asymmetric carbon atoms (Section 5-3). It assigns a unique configuration of either E or Z to any double bond capable of geometric isomerism. 

Although D-amino acids are occasionally found in nature, we usually assume the amino acids under discussion are the common L-amino acids. Remember once again that the d and l nomenclature, like the R and S designation, gives the configuration of the asymmetric carbon atom. It does not imply the sign of the optical rotation, (+) or (-), which must be determined experimentally. 

The molecular helices and propellers discussed above contain no center of chirality, and the P and M nomenclature is thus the only way of describing their absolute configuration. This nomenclature, however, is also applicable to some series of chiral compounds which display several centers of chirality. As will be discussed in Section 6, the presence in a molecule of two or more centers of chirality usually implies the existence of several stereoisomers, but steric reasons may reduce down to two the possible number of stereoisomeric forms. Thus, 2,3-epoxycyclohexanone contains two asymmetric carbon atoms, but for steric reasons only two stereoisomers, namely the (2S 3S)-(—)- and the (2/ 3/J)-( + )-enantiomer, exist the former is depicted in diagram XL [49]. 

Addition Reaction. The double bond of dehydroalanine and e-methyl dehydroalanine formed by the e-elimination reaction (Equation 6) is very reactive with nucleophiles in the solution. These may be added nucleophiles such as sulfite (44). sulfide (42), cysteine and other sulfhydryl compounds (20,47), amines such as a-N-acetyl lysine (47 ) or ammonia (48). Or the nucleophiles may be contributed by the side chains of amino acid residues, such as lysine, cysteine, histidine or tryptophan, in the protein undergoing reaction in alkaline solution. Some of these reactions are shown in Figure 1. Friedman (38) has postulated a number of additional compounds, including stereo-isomers for those shown in Figure 1, as well as those compounds formed from the reaction of B-methyldehydroalanine (from 6 elimination of threonine). He has also suggested a systematic nomenclature for these new amino acid derivatives (38). As pointed out by Friedman the stereochemistry can be complicated because of the number of asymmetric carbon atoms (two to three depending on derivative) possible. 

For achiral metallocene-based catalysts Czv and achiral Q metallocenes in Chart 2) the chain-end control is present as the only stereocontrol mechanism. It derives from the presence of an asymmetric carbon atom on the last inserted monomer. The chirality R or 5) of this atom is related to the enantiotopic face of the olefin where the insertion took place (Scheme 34). In the NMR spectrum of the polymer we lose this kind of information, as two successive insertions of the re olefin face and two successive insertions of the si face produce the same m diad (see section II.G). As a consequence, we can observe only the relative chirality between consecutive inserted monomer units (5,5 or R,R as m diads and S,R or R,S as r diads) disregarding the absolute configuration of tertiary atoms. We prefer to use the re and si nomenclature indicating the stereochemistry of the methines in the polymer chain (Scheme 35), bearing in mind that the insertion of the re propene enantioface will produce an 5 configuration on the methine. 

In general, compounds which contain asymmetric carbon atoms rotate the plane of polarization of plane-polarized light. For this reason they are said to be optically active. When the molecular symmetry is such that the optical activity of one portion of the molecule is cancelled by that of the second portion of the molecule, the compounds are said to be internally compensated and are called meso compounds. The tartaric acid with the formula (X) is such a compound and has been known as the meso-tartaric acid. The tartaric acids identified as (VIII) and (IX) have been known as d-tartaric acid and Z-tartaric acid because of the sign of their optical rotations (dextro and levo, respectively). (The nomenclature of these acids is discussed later in this chapter.) The compounds (VIII) and (IX) are non-superimposable mirror images, called enantiomorphs. The existence of such pairs of asymmetric isomers is the fundamental basis of optical activity. The asymmetry may be in either the molecular structure or the crystal structure. Asymmetric carbon atoms are not always present in optically active molecules. 

Often symmetry operations cannot be used in a simple way to classify chiral forms because, e.g., the molecule consists of a number of conformations. Therefore, independent of the symmetry considerations, a chemical approach to describe chiral molecules has been introduced by the use of structural elements such as chiral centers, chiral axis, and chiral planes. Examples for a chiral center are the asymmetric carbon atom, i.e., a carbon atom with four different substituents or the asymmetric nitrogen atom where a free electron pair can be one of the four different substituents. A chiral axis exists with a biphenyl (Figure 3.2) and chiral planes are found with cyclo-phane structures [17]. Chiral elements were introduced originally to classify the absolute configuration of molecules within the R, S nomenclature [16]. In cases where the molecules are chiral as a whole, so-called inherent dissymmetric molecules, special names have often been introduced atropiso-mers, i.e., molecules with hindered rotation about a helical molecules [18], calixarenes, cyclophanes [17], dendrimers [19], and others [20]. 

The arrangement of atoms in three-dimensional space changes both structure and reactivity and is described in several different ways in chemical substance nomenclature (see Stereochemistry Representation and Manipulation). The most common stereochemical descriptions arise from multiple bonds and from asymmetric carbon atoms. Often, as in CAS systematic nomenclature, these stereochemical descriptions are handled as separate character strings not directly part of the chemical substance name. 

The nomenclature of these acids is somewhat confused. One system is based on the parent osone that could give rise to the particular acid, L-xylosone or L-lyxosone to vitamin C, which is often termed L-xylo- (L-15 0-) ascorbic acid. (The xylo/13 0 portion is depicted in the bracket in the above formula (LXXXIV)). There are only two asymmetric carbon atoms (H-) in... 

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