Atom-based topological descriptors

Whole Molecule and Atom-Based Topological Descriptors... 

Netzeva T1 (2004) Whole molecule and atom-based topological descriptors. In Cronin MTD (ed) Predicting chemical toxicity and fate. CRC, Boca Raton FL... 

Netzeva, T.I. (2004). Whole molecule and atom-based topological descriptors, in M.T.D. Cronin and D.J. Livingstone (eds.). Predicting Chemical Toxicity and Fate, Boca Raton, FL CRC Press, pp. 61-83. 

The importance of methods to predict log P from chemical structure was described in Chapter 14, which is focused on fragment- and atom-based approaches. In this chapter property-based approaches are reviewed, which comprise two main categories (i) methods that use three-dimensional (3D) structure representation and (ii) methods that are based on topological descriptors. 

The data containing 324 descriptor values of 88 molecules was given as an input to VSMP program, to build models based on three and four descriptors, keeping the interdescriptor correlation below 0.75. The best three-descriptors model, Eq. 80, was based on descriptors 254 (atomic type E-state index), 311 (AlogP98), and 320 (2D Van der Waals surface area) with a correlation coefficient, r, of 0.8425, and the cross-validated correlation coefficient, q, of 0.8239. The correlation coefficients of the other two VSMP models, Eqs. 81 and 82 were 0.8411 and 0.8329, respectively. Significantly, the descriptors 254 and 311 were selected in all the best three-descriptors models of VSMP. The three descriptors, in the models 80, 81, and 82 were 320, 144 (Kappa shape index of order 1), and 30 (topological Xu index), respectively. 

Helguera-Morales et al. [83] used a topological sub-structural molecular design (TOPS-MODE) approach to predict the carcinogenicity of 48 nitro-aromatic compounds in female rodents. Topological descriptors are derived mainly from knowledge of the connectivity between atoms within a molecule, and are based to some extent on information on atom types and their electronic environment. The model was able to describe 79.1% of the experimental data. It was found that the carcinogenic activity of the compounds analyzed increases in the presence of a primary... 

Another set of topological descriptors is the electrotopological state indices (E-state indices) developed by Kier and Hall [26, 27]. These descriptors are based on the topological state of a particular atom with corrections for electronic interactions due to other atoms in the structure. This methodology originally devised for nonhydrogen atoms only has been extended to also include E-state indices for hydrogen atoms [28] and to also include atom-type E-state indices, for... 

Other topological descriptors do not display this disadvantage, because their definition is more general and it is possible to describe arbitrary structural patterns with the same descriptors. All topological descriptors are calculated based on the cormectivity matrix of a molecule. This matrix includes aU information about all atom-atom bonds (the so-called topology). 

Topological descriptors calculated by TOMOCOMD are divided into linear indices, bilinear indices, and quadratic indices. They are distinguished into atom-based indices and bond-based indices [Marrero-Ponce, 2004b Marrero-Ponce, Torrens et al, 2006] depending on whether they are derived from the kth power of the —> adjacency matrix ofa general graph Pt or from the fcth power of the —> edge adjacency matrix... 

Ren, B. (2002c) Novel atomic-level-based AI topological descriptors application to QSPR/QSAR modeling./. Chem. Inf. Comput. Sci., 42, 858-868. 

Ren, B. (2003a) Atom-type-based AI topological descriptors for quantitative structure-retention index correlations of aldehydes and ketones. Chemom. Intell. Lab. Syst., 66, 29-39. 

Ren, B. (2003c) Atomic-level-based AI topological descriptors for structure-property correlations. 

There are several ways in which molecular descriptors can be classified. The majority of descriptors are atom-based rather than field-based. The bulk of this review is focused on a discussion of atom-based descriptors. As the name implies, atom-based descriptors are based on individual atoms, with the description extending outward to incorporate information about the atom s environment. The descriptors are typically generated by analysis of 2D or 3D connection tables, and can include ID, 2D, or 3D information about the molecule. Atom-based descriptors include individual atoms, feature counts, substructural fragments, topological indices, atomic properties, pharmacophores (see Chapters 17 and 18 of this book), and calculated physicochemical properties. 

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