Stereodescriptor

The basic idea of specifying the priority of the atoms around a stereocenter in order to obtain a stereodescriptor is also incorporated into the most widespread structure representations, the Molfile and SMILES (see Sections 2.3.3, and 2.4.6). 

The additional stereoinformation has to be derived from the graphical representation and encoded into stereodescriptors, as described above. The stereodescriptors are then stored in corresponding fields of the connection table (Figure 2-76) [50, 51]. 

To code the configuration of a molecule various methods are described in Section 2.8. In particular, the use of wedge symbols clearly demonstrates the value added if stereodescriptors are included in the chemical structure information. The inclusion of stereochemical information gives a more realistic view of the actual spatial arrangement of the atoms of the molecule imder consideration, and can therefore be regarded as between the 2D (topological) and the 3D representation of a chemical structure. 

Fig. 5 Definition of the stereodescriptors of planar chiral ferrocenes according to Schlogl...

The 20-acetoxy derivatives of clavulones I, II and III (92-94) were reported shortly afterward with their structures being determined by spectroscopic methods [120]. A 4R and 12S (again, the incorrect 12R stereodescriptor was applied) stereochemistry in these three new compounds was deduced by the close comparability of their CD spectra with those obtained for clavulones I, II, and III (88-90). 

Zhang, Q., Aires-de-Sousa, J. Physicochemical stereodescriptors of atomic chiral centers. J. Chem. Inf. Comput. Sci. 2006, 46, 2278-2287. 

Some generic structures of /3-amino acids are shown in Fig. 6.40. Since, in /3-amino acids, two C-atoms separate the amino and carboxylate groups, there are two possible locations for attachment of a single side chain (i.e., /32 and /33), or even two or more side chains (e.g., /32,3 and /32,2,3, respectively). In a /3-peptide, these symbols can be used as prefixes, e.g., the /33/32-dipeptide in Fig. 6.40 becomes /33-HAla- /32-HVal for R=Me and R = i-Pr. The stereodescriptors (R) and (S) should be used to specify the absolute configuration at the stereogenic centers. The same rules apply to y-amino acids and y-peptides. 

With regard to the arrangement of substituents at double bonds (double-bond configuration), it is recommended that E and Z stereodescriptors rather than cis and trans stereodescriptors be used throughout. 

This system allows also for the indication of the absolute configuration of inherently chiral fullerenes by introducing the stereodescriptors f C) and f A) ( P = fullerene s = systematic numbering C = clockwise A = anti-clockwise). 

These are associated with tetrahedral and octahedral spatial distributions of atoms, and with bonds. The stereodescriptors cis and tram indicate the spatial distribution with reference to a plane defined by the molecular structure, often in relation to a double bond. 

The cis-tram stereodescriptors are acceptable for simple organic structures and they have been used also to describe spatial distribution in octahedral and square-planar structures. However, they are not adequate to distinguish all possibilities. The system that is currently recommended for complexes is described in more detail in the Nomenclature of Inorganic Chemistry, Chapter 10. 

The examples below further demonstrate the use in organic nomenclature of the stereodescriptors described above. 

Names of cyclised (hemi-acetalised) aldoses and ketoses contain the infixes pyran or furan to indicate the six- or five-membered heterocyclic structure and a stereodescriptor, a or p, to indicate the configuration of the anomeric or hemi-acetal carbon atom. 

The stereodescriptors d and l are used with reference to the d configuration of glyceraldehyde. 

Compounds similar to glycerol, called sphingoids, are derivatives of sphinganine (o-erj t/iro-2-aminooctadecane-l,3-diol). The trivial name sphinganine implies the stereochemistry the use of the stereodescriptor D-erythro in the systematic name is to be noted. 

The assignment of descriptors and configuration is sometimes arbitrary, at best, when based on model structures and pseudo-atom coordination numbers. A more explicit stereochemical notation is achieved by using this notation, which states within the stereodescriptor the model structure on which the notation is based. In this notation the pseudo-square pyramidal structure is [5PF-5-14-C(i )]. This structure can be expected to result in geometric isomers when one of the... 

The stereodescriptors endo and exo are used to distinguish between the positions of a substituent beneath or outside the concave area of a bent molecule. For example, in the major product of the reduction of norbomanone with Li BH (sec-Bu)3 (Formula A in Figure 10.10) the added H atom is oriented exo and the OH group obtained endo. 

Fig. 13.46. Explanation of the anti-selectivity of the Ivanov reaction of Figure 13.45 by means of the Zimmerman-Traxler model. The stereodescriptors Re and Si are defined as follows. Suppose you are looking down on the plane of an alkene, in which an sp2-hybridized C atom is connected to three different substituents. You are on the Re side of the double bond if the Cahn-Ingold-Prelog priorities of these substituents decrease going clockwise, and on the Si side otherwise.

What is the difference between the descriptor pairs RelSi and re/sP Which of these two stereodescriptor pairs can be used to describe the two faces of the planar part of the structures of the following compounds ... 

Nateglinide is an orally administered antidiabetic. Assign suitable stereodescriptors to describe the structure and determine the amino acid from which it is derived. 

How many isomers are there of diamminedichloridoplatinum(II), [PtCl2NH3)2] Determine the symmetry elements and point groups for all isomers and assign appropriate stereodescriptors. 

Deduce the symmetry point groups of all the isomers of [CrCl2(NH3)4]+ and assign a precise stereodescriptor for each isomer. 

What other stereodescriptor can be used to describe the configuration of ( a)-l,3-dichloroallene unambiguously ... 

Determine all the stereoisomers of the coordination entity shown below and assign appropriate stereodescriptors. 

How many stereoisomers are there of bis(2-aminoethanethiolato-AT,S)-nickel(II) Give appropriate stereodescriptors for all the isomers. 

In the N-oxide of loperamide (an antidiarrheal) the hydroxy group and the oxide oxygen have a trans relationship. Draw the structure in a chair form and determine whether the molecule is chiral. Which stereodescriptors must be added to the systematic name to exactly describe the configuration ... 

Different cyclic products are formed in the double Michael addition of malonic acid ethyl methyl ester to ( vE)-l,5-diphenylpenta-l,4-dien-3-one under basic conditions. Label the stereogenic units in the reaction products with the appropriate stereodescriptors. 

Maleic anhydride is subjected to a cycloaddition reaction with cyclopenta-1,3-diene. What products would be produced and which stereodescriptors could be used to completely describe these compounds Are the products chiral ... 

Assign suitable stereodescriptors to the dopamine reuptake inhibitor brasofensine. 

Describe the base induced elimination reactions of the deuterated compounds represented by the following formulae and assign appropriate stereodescriptors to the resulting olefins. (Note that as well as the hydrogen atom the deuterium atom can also be abstracted from these compounds.)... 

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