Molecular fragments coding

A particularly good selection of physical properties may be spectra, because they are known to depend strongly on the chemical structure. In fact, different types of spectra carry different kinds of structural information, NMR spectra characterize individual carbon atoms in their molecular environment. They therefore correspond quite closely to fragment-based descriptors, as underlined by the success of approaches to predict NMR spectra by fragment codes (see Section 10.2.3). 

The similarity matrices are constructed by one in-house program developed inside CHIRBASE using the application development kit of ISIS. They contain the similarity coefficients as expressed by the Tanimoto method. In ISIS, the Tanimoto coefficients are calculated from a set of binary descriptors or molecular keys coding the structural fragments of the molecules. 

The molecular surface concept is not only useful for a representation of the bulkiness and the shape of molecules. These surfaces can also be used as screens for the visualization of many properties by means of color coding techniques. Color coding is a popular means of displaying scalar information on a surface. " " Every three-dimensional scalar or vector field that may be generated on the basis of the position of atomic or molecular fragments can be visualized by color coding on a given surface. 

The nonvisual shape similarity measures of molecules as well as molecular fragments, using the numerical shape code method, provide the basis for a shape complementarity measure. A simple transformation of the local shape codes generates a representation that is suitable for a direct evaluation of local shape complementarity. 

The ready communication of structural information is fundamental to the development of chemistry. The most universally understood form of such information is the chemical structure diagram, such as that illustrated in Figure 1. However, it is frequently Inconvenient to convey structural information directly (e.g., in conversation), so a number of other methods of representing chemical structures have been developed to satisfy a variety of needs. These methods include nomenclatures, notations, connection tables, adjacency matrices, molecular fonnulas, and fragment codes [1 2]. 

For 99 mutagens (a subset of the 160 compounds above), the WLN-derived fragment codes and several of the molecular connectivity indices described by Kier and Hall (55) were used to derive a regression equation (using multiple linear regression analysis) which related the revertants per nanomole (expressed as log / /nmol) to 10 WLN keys and 5 molecular connectivity indices. The resulting equation is given in Table IV it explains about 75% of the variance in the data (55<3). 

Fig. 7. Graphical representations of (a) the Highest Occupied Molecular Orbital (HOMO) and (b) the Lowest Unoccupied Molecular Orbital (LUMO) for ranitidine. It is possible, in the ordinarily visible color-coded data not shown here, to distinguish the strong localization (a) of the HOMO to the sulfur atom and adjacent nitroethyleneamine fragment and the contrasting localization (b) of the LUMO to the nitroethylenearnine fragment. Neither the LUMO not HOMO appear to have contributions from the dimethylaminomethyl-suhstitiited furan.

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