Stereoisomer descriptors

Do not capitalize chemical names or nonproprietary drug names unless they are at the beginning of a sentence or are in a title or heading. In such cases, capitalize the first letter of the English word, not the locant, stereoisomer descriptor, or positional prefix. (See Chapter 12, Names and Numbers for Chemical Compounds .)... 

Figure 2-74. Basic stages for describing a stereoisomer by a permutation descriptor. At the stereocenter, the molecule is separated into the skeleton and its ligands. Both are then numbered independently, with the indices of the skeleton in italics, the indices of the ligands in bold.

Figure 2-75. Determination of a permutation descriptor of a stereoisomer after reflection at the stereocenter...

However, the descriptors cannot be considered independently as there is no free rotation around the double bond, In order to take account of this rigidity, the descriptors of the two units have to be multiplied to fix a descriptor of the complete stereoisomer. 

Many classes of natural product possess heterocyclic components (e.g. alkaloids, carbohydrates). However, their structures are often complex, and although structure-based names derived by using the principles outlined in the foregoing sections can be devised, such names tend to be impossibly cumbersome. Furthermore, the properties of complex natural product structures are often closely bound up with their stereochemistry, and for a molecule containing a number of asymmetric elements the specification of a particular stereoisomer by using the fundamental descriptors (R/S, EjZ) is a job few chemists relish. 

With the development of accurate computational methods for generating 3D conformations of chemical structures, QSAR approaches that employ 3D descriptors have been developed to address the problems of 2D QSAR techniques, e.g., their inability to distinguish stereoisomers. The examples of 3D QSAR include molecular shape analysis (MSA) [34], distance geometry [35,36], and Voronoi techniques [37]. 

When dealing with reactions leading to stereoisomeric products we have the additional complication that descriptors such as enantiomeric (diastereomeric) excess and enantiomeric (diastereomeric) ratio are used to describe product purities. The evaluation of RME for a specific stereoisomer, say the R enantiomer, is exactly as above using the connecting relationships for the fraction of each product shown below. 

There are two stereoisomers of bis(2-aminoethanethiolato-JV,S)nickel(II). These have the stereodescriptors (SP-4-1) and (SP-4-2). (The descriptors trans and cis are equally unambiguous here. Their use is, however, not recommended, since there are other square planar coordination compounds where these descriptors cannot be used.)... 

In the crossed aldol reaction between acetaldehyde and propiophenone, two chirality centres are created and consequently, four stereoisomers will be produced. Compounds A and B are enantiomers of each other and can be described with the stereo descriptor u. Similarly, C and D are enantiomers and are /-configured. Since both starting materials are achiral, without the use of a chiral base or chiral auxiliary, racemates will be produced. Likewise the choice of base, the addition of a Lewis acid and the reaction conditions used to form the enolate can control which diastereomer is preferentially formed. If the Z enolate is formed, the u product is the preferred product, whilst the E enolate yields predominately the / product. 

Figure 1.6. Schlegel diagrams of two stereoisomers of tetrakis[( )-l-phenylbutyl] l,2 56,57-bis (methano)[70]fullerene-71,71J2,72-tetracarboxylate.35 54 The two types of stereogenic elements (inherently chiral addition pattern and stereogenic centers in the ester groups) are specified independently of each other. As can be seen from the descriptors (S,S,S,S, C) and (S fA), the depicted molecules are diastereoisomers.

When a molecule contains only one chiral center, the two stereoisomers are known as enantiomers. These may be referred to or labeled using the configurational descriptors as either R rectus meaning righthanded) or S (sinister meaning left handed), or alternatively, D (dextrorotatory) or l (levorotatory). The D and l configurational descriptors are... 

A word of caution should be added with respect to Chemical Abstracts, as far as chirality assignments of homoannular substituted ferrocene derivatives are concerned. Until the 8th collective index, only (-f) and (—) are found as chirality indicators. For quite a long time, no descriptors were given at all, only the remark stereoisomer , followed by the registry number, which does not allow identification of a compound easily. This fact is in sharp contrast to the claims of Chemical Abstracts Service authors that they would consequently use Schlogl s central descriptors [20, 21]. Since volume 114, the (R, S ) nomenclature for ferrocene derivatives begins to appear, but its application is not very consequent, at least at the time where the book was written, and it is advisible to examine the orginal article rather than trust Chemical Abstract s descriptors. 

The appropriate representation of a molecule with RDF descriptors finally depends on the question of what the term similarity should describe in the given context. Let us have a look at the following example. Figure 5.8 shows three possible configurations of stereoisomers for a Ruthenium complex with sulfur dominated coordination sphere, a compound that serves as a model for nitrogenase. 

FIGURE 5.9 (a) Molecular Cartesian RDF descriptors for the stereoisomers shown in... 

The local Cartesian RDF descriptors of the stereoisomers are generally more similar among each other than the molecnlar ones. They exhibit particularly two patterns that describe the different ligand sphere of the stereoisomers in the distance... 

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