Descriptor molecular fragments

In this chapter, the genesis of SMILES-based descriptors (as well as perspectives of utilization of these characteristics for QSPR/QSAR analyses) is discussed. We concluded that in fact the SMILES-based optimal descriptors are derivatives of the graph-based optimal descriptors. In fact the SMILES-based descriptors are calculated with scheme that is similar to the well-known additive scheme (Zinkevich et al., 2004), but instead of contributions for the molecular fragments (chemical elements, different kinds of cycles, covalent bonds, etc.) contributions for the SMILES fragments (c, C, n, N, Cl, Br, =,, etc.) are using. 

Molecular descriptors vary gready in both their origins and their applications. They come from both experimental measurements and theoretical computations. Typical molecular descriptors from experimental measurements include logP, aqueous solubility, molar refractivity, dipole moment, polarizability, Hammett substituent constants, and other empirical physicochemical properties. Notice that the majority of experimental descriptors are for entire molecules and come directly from experimental measurements. A few of them, such as various substituent constants, are for molecular fragments attached to certain molecular templates and they are derived from experimental results. 

Table 2.5 defines the 40 molecular descriptors and provides their values. Figure 2.1 provides further definition of the different types of molecular fragments used while Figure 2.2 provides further definition of the hydrogen bonding and biphenyl ring corrections. Simamora and Yalkowsky (1994) consider the values in parentheses in Table 2.5 insignificant, based on the statistical analysis used to derive the molecular descriptor values. 

Niculescu, S.P., Kaiser, K.L.E., and Schultz, T.W., Modeling the toxicity of chemicals to Tetmhymena pyri-formis using molecular fragment descriptors and probabilistic networks, Arch. Environ. Contamination Toxicol., 39, 289-298, 2000. 

These are - electronic descriptors defined in terms of atomic charges and used to describe electronic aspects both of the whole molecule and of particular regions, such as atoms, bonds, and molecular fragments. Charge descriptors are ealculated by - computational chemistry and therefore can be considered among - quantum-chemical descriptors [Lowe, 1978 Streitweiser, 1961],... 

These total charge descriptors can also be calculated restricted to a molecular fragment as well as to a functional group. 

Empirical descriptors can be a few user-defined values for discriminating among special molecular fragments or counting local specific atom/fragment occurrences within a molecule. 

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