Nomenclature chirality center configurations

Aldoses with at least three carbons and ketoses with at least four carbons contain chiral centers (Chapter 4). The nomenclature for such molecules must specify the configuration about each asymmetric center, and drawings of these molecules must be based on a system that clearly specifies these configurations. 

There is another point of nomenclature that must be discussed, namely where a chiral center is involved. Taking the simple case of 2-butanol, CH3CH(OH)CH2CH3, we can explain the point as follows (Scheme 1). Two configurations are possible at the chiral center. In both the R and the S series, three conformations are possible. The +sc form in the R series and the -sc form in the S series are enantiomers and their free energies must be the same under achiral conditions. However, the - sc form in the R and that in the S series differ in free energies. Therefore, it is not sufficient to call a conformation -sc if a chiral center is involved. In this case we may have to call such conformations - sc(R) and — sc(S) to distinguish them. 

Another system of specifying configuration around a chiral center is the RS system, which is used in the systematic nomenclature of organic chemistry and describes more precisely the configuration of molecules with more than one chiral center (see p. 18). 

In response to this nomenclature dilemma, the Cahn-Ingold-Prelog (IUPAC, International Union of Pure and Applied Chemistry) system of nomenclature was developed and is now the standard mediod to specify the relative configuration of chiral centers in molecules. Each chiral center will have two possible mirror-image configurations, which are designated as eidter R or S. 

Note also that the D,L system of carbohydrate nomenclature describ the configuration at only one chirality center and says nothing about i configuration of other chirality centers that may be present. The advanti of the system, though, is that it allows us to relate one sugar to anotl rapidly and visually. 

The stereochemistry of side-chain substituents is described by the sequence rule procedure, where any chiral centers formed by substituents at C-20 or above are assigned the (R) or (S) configuration. This designation, when employed, precedes the entire nomenclature name (see Section 3.5.2.2). For brevity, the side-chain stereochemistry will not be described in further detail. 

Isoleucine and threonine both have two chiral centers. According to official nomenclature the names L-isoleucine and L-threonine both designate only one optically active diastereoisomer. The mirror images are named D-isoleucine and o-threonine, whereas the diastereoisomers are named l-and D-alloisoleucine and l- and D-allothreonine. The configurations of L-isoleucine and L-threonine are shown in the formulas in Table I. The table also contains notation of the configuration at the two centers according to the R,S system and according to traditional nomenclature for amino acids (lUPAC-IUB, 1975). 

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]. 

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