Topological Structure Codes

An enhancement of the simple substructure approach is the Fragment Reduced to an Environment that is Limited (FREL) method introduced by Dubois et al. [7] With the FREL method several centers of the molecule are described, including their chemical environment. By taking the elements H, C, N, O, and halogens into account and combining all bond types (single, double, triple, aromatic), the authors found descriptors for 43 different FREL centers that can be used to characterize a molecule. 

One of the most widely used - and successful representations of the constitution, the topology, of a molecule is the HOSE code (Hierarchical Ordered description of the Substructure Environment) [9]. It is an atom-centered code taking into account 

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Each species is also denoted by a three-letter structure code that describes the framework topology (connectivity, channel dimensionality etc). Examples are given in Table 9.1 common structures of some representative zeolites are shown in Figure 9.6. 

In this chapter, we outline the principles of classification, coding and decoding, and estimating the complexity of reaction mechanisms, as well as develop some approaches to identification of the topological structure of linear mechanisms. 

Besides immediate practical applications in fields such as drug design, molecular surfaces contribute to the transformation of modernizing the conceptual arsenal of chemistry, long dominated by line drawings of chemical bonds of structural formulas. Molecular surfaces have led to a true appreciation of the three-dimensional aspects of molecules, important in all branches of chemistry. Precise methods for the analysis of the shapes of these surfaces are available using the topological shape codes and provide tools for the numerical evaluation of such elusive but important properties as measures of molecular similarity and shape complementarity. 

TOPER AG (the Topological Fragment Code Generator program for chemical structure access to the Derwent patents data base) (26). 

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 problem of perception complete structures is related to the problem of their representation, for which the basic requirements are to represent as much as possible the functionality of the structure, to be unique, and to allow the restoration of the structure. Various approaches have been devised to this end. They comprise the use of molecular formulas, molecular weights, trade and/or trivial names, various line notations, registry numbers, constitutional diagrams 2D representations), atom coordinates (2D or 3D representations), topological indices, hash codes, and others (see Chapter 2). 

However, we should emphasize that the NBO/NRT concepts of hybridization, Lewis structure, and resonance differ in important respects from previous empirical usage of these terms. In earlier phases of valence theory it was seldom possible to determine, e.g., the atomic hybridization by independent theoretical or experimental procedures, and instead this term became a loosely coded synonym for the molecular topology. For example, a trigonally coordinated atom might be categorized as sp2-hybridized or an octahedrally coordinated atom as d2sp3-hybridized, with no supporting evidence for the accuracy of these labels as descriptors of actual... 

The connectivity (topology) of the zeolite framework is characteristic for a given zeolite type, whereas the composition of the framework and the type of extra-framework species can vary. Each zeolite structure type is denoted by a three-letter code [4], As an example, Faujasite-type zeolites have the structure type FAU. The pores and cages of the different zeolites are thus formed by modifications of the TO4 connectivity of the zeolite framework. 

The concept of structure comparability is of practical use in the search of correlations between topological indices and molecular properties. It does not directly contain a numerical comparability index (through the authors23) use this term for what we called above comparability code). Two such indices proposed here, as a modification of the M, index, and are denoted as 3 and 3 ... 

From their definitions, one may admit that topological indices may code two structural factors, namely, the size and the shape of the molecule. This assumption is proved by calculating 94) the schemes (B) in Figure 2 for the 36 polyalkylcyclohexanes with 6-10 carbon atoms, and for a subseries of 22 polyalkylcyclohexanes with 10 carbon atoms (resulting in scheme (C)). The schemes (A)-(C) corroborated with the... 

The second variant of QSAR is the use of actual structural descriptors, such as molecular orbital indices or topological codes, to define numerically the structure of a molecule and to find linear relationships with numerical biological data (Kier and Hall, 1976, 1992). 

It should be stressed that the coding for the formation of these topologically complex molecules needs to be carefully controlled in order to obtain the desired structures. To illustrate this, consider ligand 7.59, which contains two didentate metal-binding domains. This might be expected to react with octahedral metal ions to give a triple-helical dinuclear complex. Reaction with iron(n) does indeed give a species of stoichiometry [Fe2(7.59)3]4+ however, the crystal structure reveals that an untwisted complex, 7.60, has been formed. 

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