Stereocenter

If compounds have the same topology (constitution) but different topography (geometry), they are called stereoisomers. The configuration expresses the different positions of atoms around stereocenters, stereoaxes, and stereoplanes in 3D space, e.g., chiral structures (enantiomers, diastereomers, atropisomers, helicenes, etc.), or cisftrans (Z/E) configuration. If it is possible to interconvert stereoisomers by a rotation around a C-C single bond, they are called conformers. 

Figure 2-71. The ordered list of 24 priority sequences of the ligands A-D around a tetrahedral stereocenter, The permutations can be separated into two classes, according to the Cl P rules the R stereoisomer is on the right-hand side, and the S stereoisomer on the left.

In order to handle the stereochemistry by permutation groups, the molecule is separated at each stereocenter into a skeleton and its ligands (Figure 2-74). 

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...

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). 

A molecule editor can draw a chemical structure and save it, for example as a Molfile. Although it is possible to include stereochemical properties in the drawing as wedges and hashed bonds, or even to assign a stereocenter/stereogroup with its identifiers R/S or E/Z), the connection table of the Molfile only represents the constitution (topology) of the molecule. 

Similarly the stereobonds" can be defined and added to the bond list in the fourth column of the CT. A single bond acquires the value of 0 if it is not a "stereobond, 1 for np (a wedged bond). 4 for either up or down, and 6 for down (a basbed bond), The cisjtrans or E[Z configuration of a double bond is determined by the x,y.2 coordinates of the atom block if the value is 0, Tf it is 3, the double bond is either cis or tmns. In the bond block of our example (Figure 2-76), the stereocenter is set to 1 (up) at atom 6 (row 6, column 4 in the bond block), whereas the configurations of the double bonds are determined by the x,y coordinates of the atom block. 

Figure 2-77. Determination of parity value, a) First the structure is canonicalized. Only the Morgan numbers at the stereocenter are displayed here, b) The listing starts with the Morgan numbers of the atoms next to the stereocenter (1), according to certain rules. Then the parity value is determined by counting the number of permutations (odd = 1, even = 2).

Stereochemistry can also be expressed in the SMILES notation [113]. Depending on the clockwise or anti-clockwise ordering of the atoms, the stereocenter is specified in the SMILES code with or respectively Figure 2-78). The atoms around this stereocenter are then assigned by the sequence of the atom symbols following the identifier or (g). This means that, reading the SMILES code from the left, the three atoms behind the identifiers ( ) or ( )( )) describe the stereochemistry of the stereocenter. The sequence of these three atoms is dependent only on the order of writing, and independent of the priorities of the atoms. 

First, both the skeleton and the ligands at a stereocenter have to be numbered independently of each other. The sites of the skeleton can be numbered arbitrarily but then this numbering has to remain fixed all the time in any further operations. The atoms directly bonded to the stereocenter have to be numbered according to rules such as the CIP rules or the Morgan Algorithm (Figure 2-79). 

However, as the descriptor oFthc eutirc steveoisoraer is obtained by multiplicatiou of the individual descriptors, again a value of (-(-1 is obtained. Thus, as desired, the stereocenter of a double bond does not change through rotation of a molecule. 

Stereochemical strategies The transform selection is guided by stereocenters that have to be removed in retrosynthesis. The user has to select strategic stereo-centers. 

Absolute Stereochemistry Absolute stereochemical assignment of each stereocenter (R vs S) Cahn-Ingold-Prelog Convention (sequence rules)... 

Diastereomers which differ at a single stereocenter are called epimers. 

Chemical conversion of compounds to intermediates of known absolute configuration is a method routinely used to determine absolute configuration (86). This is necessary because x-ray analysis is not always possible suitable crystals are required and deterrnination of the absolute configuration of many crystalline molecules caimot be done because of poor resolution. Such poor resolution is usually a function of either molecular instability or the complex nature of the molecule. For example, the relative configuration of the macroHde immunosuppressant FK-506 (105) (Fig. 8), which contains 14 stereocenters, was determined by x-ray crystallographic studies. However, the absolute configuration could only be elucidated by chemical degradation and isolation of L-pipecoUc acid (110) (80). 

Antineoplastic Drugs. Cyclophosphamide (193) produces antineoplastic effects (see Chemotherapeutics, anticancer) via biochemical conversion to a highly reactive phosphoramide mustard (194) it is chiral owing to the tetrahedral phosphoms atom. The therapeutic index of the (3)-(-)-cyclophosphamide [50-18-0] (193) is twice that of the (+)-enantiomer due to increased antitumor activity the enantiomers are equally toxic (139). The effectiveness of the DNA intercalator dmgs adriamycin [57-22-7] (195) and daunomycin [20830-81-3] (196) is affected by changes in stereochemistry within the aglycon portions of these compounds. Inversion of the carbohydrate C-1 stereocenter provides compounds without activity. The carbohydrate C-4 epimer of adriamycin, epimbicin [56420-45-2] is as potent as its parent molecule, but is significandy less toxic (139). 

Most substrates, with the exception of hydroxypymvate, have a threo configuration of hydroxyl groups at the C-3 and C-4 positions (139). The new stereocenter formed in TK-catalyzed addition is formed in the threo configuration with high diastereo-selectivity (151). Using TK-catalyzed condensations of hydroxypymvic acid with a number of aldehydes a practical preparative synthesis of L-idose [5934-56-5], L-gulose [6027-89-0], 2-deoxy-L-xylohexose, and... 

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