Representation of Stereochemistry

The Morgan algorithm 5> is a device used by the Chemical Abstracts Service for assigning indices to the nodes of constitutional formulas whose H-atoms have been omitted, i. e. their reduced graphs. If the indices of all atoms are needed, e.g. for the representation of stereochemistry, an additional procedure is needed for establishing those for the H-atoms. Constitutional symmetry is not indicated directly by Morgan indices. 

The structures shown in Figure 3.5 can give rise to 32, 2,048, and 512 different stereoisomers, respectively, and do not accurately represent the chemical names displayed below. It is very common that the representation of stereochemistry for both amino acids and steroids is not reported in publications. Caution must be used with the generation of the N2S engine structure dictionary from representations that omit stereo configurations, for example, from nonstereo SMILES notation. 

Although drawings provide a pictorial representation of stereochemistry, they are difficult to translate into words. Thus, a verbal method for indicating the three-dimensional arrangement of atoms, or configuration, at... 

Conventions for the representation of stereochemistry are also worth noting. A heavy or bold bond indicates that a substituent is pointing toward you, out of the plane of the paper. A hashed bond indicates that a substituent is pointing away from you, behind the plane of the paper. Sometimes a dashed line is used for the same purpose as a hashed line, but the predominant convention is that a dashed line designates a partial bond (as in a transition state), not stereochemistry. A squiggly or wavy line indicates that there is a mixture of both stereochemistries at that stereocenter, i.e., that the substituent is pointing toward you in some fraction of the sample and away from you in the other fraction. A plain line is used when the stereochemistry is unknown or irrelevant. 

Another important disadvantage is the insufficient representation of stereochemistry enantiomers show exactly the same autocorrelation descriptor values. 

Two-dimensional representations alternative to the molecular graph are the linear notation systems, for example, Wiswesser Line Notation system (WLN) [Smith and Baker, 1975], SMILES [Weininger, 1988, 1990, 2003 Weininger, Weininger et al., 1989 Convard, Dubost et al., 1994 Hinze and Welz, 1996], and SMARTS (SMART - Daylight Chemical Information Systems, 2004). CAST (CAnonical representation of STereochemistry) is a method that gives a linear notation that canonically represents stereochemistry around a specific site in a molecule [Satoh, Koshino et al, 2000, 2001, 2002],... 

In these "sawhorse representations of stereochemistry, the part of the molecule on the lower left is in front of the part on the upper right. 

Three chapters about online databases follow. Clemens Jochum s concerns the construction of the Beilstein Online database. Of particular interest are the complete representation of stereochemistry and the replacement of bond orders by electronic information, allowing a global, and unique, representation of tautomers. Ole Norager describes the ECDIN project, in which data has been collected on environmental chemicals and made accessible online. Gerry vander Stouw shows how the Chemical Abstracts Registry System Enhancements Feasibility Study project identified aspects of the CAS structuring conventions which create problems for users and he considers the improvements which may be recommended. 

A. Dietz, C. Eiorio, M. Habib and C. Laurenco, Representation of Stereochemistry using Combinatorial Maps, in Discrete Mathematical Chemistry, DIMACS Series in Discrete Mathematical and Theoretical Computer Science, Vol. 51, eds. P. Hansen, PW. Eowler and M. Zheng, American Mathematical Society, Providence, RI, 2000, pp. 117-128. 

Structural drawings provide a visual representation of stereochemistry, but a written method for indicating the three-dimensional arrangement, or configuration, of substituents at a chirality center is also needed. The method used employs a set of sequence rules to rank the four groups attached to the chirality center and then looks at the handedness with which those groups are attached. 

A number of formats are in use that can represent stereochemical information. We do not discuss 3D formats here, but rather concentrate on 2D representations of stereochemistry. All examples in this section refer to compound 21. 

H. W. Davis, Computer Representation of Stereochemistry of Organic Molecules , Birkhaeuser Verlag, Basel. 1976. 

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