Representation molecular structure stereochemistry

The drawing of a molecular structure will show all the bond connectivities between neighbouring atoms and, if a stereochemistry representation is used, the configuration and the conformation of the molecule. The NMR experiment is based on the detection of spin systems and consequently the molecular structure can be defined in terms of spin systems using chemical shifts, coupling networks and, for stereochemical information, the relaxation times of the NMR active nuclei. 

W.T. Wipke H) first achieved the canonicalization of a molecular structure representation in a computer program that includes all aspects of stereochemistry. In some other schemes, stereochemistry is not invoked to aid in the mambering of the atoms. Such schemes are incomplete. If we relegate stereochemistry to a footnote and the numbering of the atoms and the connection tables of two isomers can be the same, then we lose most of the above-stated advantages of canonicalizing. 

The usual chemical structure representation (CSR) of a compound in chemical information systems is the connection table, adjacency matrix, linear notation, or structural lists which describe the molecular structure. The CSR contains all the information required to characterize fully the chemical structure of a compound, i.e., the chemical nature of atoms, bonding information, stereochemistry, and geometry (see Structure Representation). 

About 20 years ago, the theory of the be- and r-matrices, a global algebraic model of the logical structure of constitutional chemistry was formulated. This theory is the first direct mathematical approach to chemistry which also accentuates its dynamic aspect. The representation by mathematics comprises the individual objects of chemistry and also their relations, including their interconvertibility by chemical reactions. A decade later, the theory of the chemical identity groups was published in a monograph. It is a unified theory of stereochemistry that is primarily devoted to relations between molecular systems. 

In these considerations on STL structure, one important aspect was not taken into account so far, namely, that of explicit stereochemistry. The STL database consists, as mentioned above, of 2D representations in the form of the SMILES string. It is at present not possible to include structural features based on molecular geometry, such as shape, charge distribution, etc. in our investigation on the molecular properties of STLs as a whole, since this would necessitate the generation of 3D structures with the correct stereochemistry for each of the 4861 molecules, which would only be possible by... 

Chemical Abstracts Service Information System Combinatorial Chemistry Computer Graphics and Molecular Modeling Factual Information Databases Online Databases in Chemistry Reaction Classification Stereochemistry Representation and Manipulation Structural Similarity Measures for Database Searching Structure and Substructure Searching Structure Representation Synthesis Design. 

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