Coding of chemical structures

The Hosoya index was applied 2,60 63) to correlations with boiling points, entropies, calculated bond orders, as well as for coding of chemical structures. 

Examples of some of the oldest analytical databases are given in Table 7.1. At present, databases that comprise several spectromet-ric methods, such as SDBS (Spectral database for organic compounds, AIST), exist and in SciFinder (CAS), several databases are combined to reveal more than 42 mUhon of spectra. Apart from representation of the analytical measurements in the computer, the coding of chemical structures is an important aspect of constructing analytical databases. 

Over and beyond the representations of chemical structures presented so far, there are others for specific applications. Some of the representations discussed in this section, e.g., fragment coding or hash coding, can also be seen as structure descriptors, but this is a more philosophical question. Structure descriptors are introduced in Chapter 8. 

Four main approaches have been suggested for the representation of chemical structures in machine-readable form fragment codes, systematic nomenclature, linear notations, and connection tables. 

FIGURE 6.3 Twenty standard amino acids used for cluster analysis of chemical structures. For the three-letter codes, see Table 6.1. 

Fig. 37 a Schematic diagram that illustrates the equilibrium shifting driven by folding and ligand binding. The sequences are color coded, b Chemical structure of oligomers used in the metathesis reaction... 

Sachse, S., Rappert, A. and Galizia, C. G. (1999). The spatial representation of chemical structures in the antennal lobe of honeybees steps towards the olfactory code. European Journal of Neuroscience 11 3970-3982. 

Note that these rules do not apply for the coding of salts and isomers, although the full SMILES language and variants can handle all types of chemical structure. These rules are illustrated in the examples below. 

There are several linear canonical notations for the input of chemical structures into the computer notable among these are the Wiswesser line notation [226] and the IUPAC notation [227], which are used in industrial information systems. In order to achieve a canonical notation, a large number of rules are necessary, more than three hundred in the Wiswesser line notation [226]. Furthermore, the resulting notation is quite arbitrary and very far from the usual practice of a chemist for example, acetone is 1V1 in the Wiswesser notation. In conclusion, both coding a formula and reading a coded formula in the Wiswesser notation require highly trained chemists. 

Balaban, A.T, Mekenyan, O. and Bonchev, D. (1985b). Unique Description of Chemical Structures Based on Hierarchically Ordered Extended Connectivities (HOC Fh-ocedures). III. Topological, Chemical, and Stereochemical Coding of Molecular Structure. J.Comput.Chem., 6, 562-569. 

If the odors of specific objects translate into unitary percepts, which constitute the basic entities in linguistic descriptions of olfaction, then the question follows as to whether these unitary percepts take shape at the level of the receptor neurons or in the olfactory bulb or elsewhere in the brain. That question remains unanswered, as of this writing. Because the sense of smell does not correlate perfectly with externally monitored patterns of electrical response from the receptor neurons or the olfactory bulb, the nature of olfactory coding remains unknown. Outside the laboratory unitary percepts rarely equate to pure compounds. Two vocabularies coexist, one of smells (which varies from individual to individual, and which refers to other inputs besides olfaction) and the other of chemical structures. 

Barcodes are among the best known codes for a large variety of items. Many libraries rely on barcodes for the automated storing and tracking of books, and most repositories of pharmaceutical companies use barcodes to encode their test compounds. Therefore, it is not surprising that this technique has also been used for the encoding of chemical/structural informahon during synthesis. 

The idea of using Ch(G) in chemical documentation work for the coding of molecular structure had to be abandoned because of the occurrence of isospectrai mdecular graphs [20]. 

Consider a conventional encoding of chemical structures in C-NMR spectroscopy as introduced with the so-called HOSE code (hierarchically ordered spherical description of environment). Table 7.4 contains some symbol descriptions of this code. 

As a general rule, in the representation of chemical structures, the hydrogen atoms are not coded at all. If necessary, for example, for graphical representation of a molecule, hydrogen atoms can be added by a suitable algorithm automatically. 

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