Stereochemical stereodescriptors

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. 

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... 

Retrieve the Registry File substance and parse its stereodescriptor into components that identify the stereoparent and describe the topological and stereochemical modifications. 

CAS has undertaken a multi-year effort to renovate the Registry System. As part of this effort, we are currently engaged in adding atom/bond specific stereodescriptors to the connection tables of stereospecific substances already on the Registry File. These extensions will, in turn, permit us to enhance structure display and substructure search to use accurately the stereochemical information available. 

In another approach (see NMR Data Correlation with Chemical Structure),three-dimensional (3D) substructure descriptors are used as a basis for the prediction. In this case the distribution function is simplified and a subsequent analysis is not required. This extension of the HOSE code is based on the ability to count the total number of steric interactions over a three-, four-, and five-bond sphere and additional parameters to describe the axial and equatorial substitution pattern for each atom. In the simple case of cis/trans ksomerism the number of interactions is calculated by means of the display coordinates. More complex situations are described by up/down bonds in this case the calculation of the number of steric interactions for each atom is performed by comparison of the query structure with carefully selected references from a library of ring skeletons. Figure 6 exemplifies the method. The discussion of the stereochemical effects is focused on the two diastereotopic methyl groups at position 4. The experimental shift values are 22.0 and 33.6 ppm. The prediction without stereodescriptors results in 27.4 ppm for both atoms (Figure 6, upper part). If the stereochemical effects are considered, the predicted shifts (21.5 and 33.5 ppm) deviate insignificantly from the experimental values (Figure 6, bottom). 

The first class uses manually assigned stereodescriptors (e.g., CIP or template-based) as additional attributes of the graph nodes and edges to further refine the symmetry classes. The algorithms then proceed with the selection of canonical numberings as in the non-stereochemical case. This method works as well as the original stereochemical descriptors describe the structure, but note the problems cited above for the CIP system. 

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