Fragments Atom-Centred

The software program SMILOGP for the calculation of logP is based on the Broto-Moreau-Vandycke hydrophobic constants and the SMILES notation for the recognition of molecule atom-centred fragments [Convard etal, 1994]. 

Adamson, G.W., Lynch, M.F. and Town, W.G. (1970). Analysis of Structural Characteristics of Chemical Compounds in a Large Computer-based File. Part II. Atom-Centred Fragments. J.Chem.Soc., (C), 3702-3706. 

Figure 1 Examples of atom, bond and ring-centred fragments investigated at Sheffield University. Bonds marked r are explicitly ring bonds.

The respective atom and fragment values have been tabulated (e.g. Seydel and Schaper, 1979) the major disadvantage of these methods, however, is the neglect of the fact that volume and surface depend on the conformation of the molecule. The solvent-accessible volume and surface area depend on the size of the solvent molecule, generally water, and this is considered additionally. The solvent-accessible surface is defined as the locus of the centre of a spherical solvent rolled over the van der Waals surface of the solute. 

From a purely formal point of view the molecules are assemblies of atoms and bonds, consequently the definition of fragments may be done in terms of these constituents. We can imagine fragments as ensembles of (a) atoms, (b) bonds. Evidently in the first case the bonds linking the fragments should be broken, while in the second case the atomic centres at the borderline of two fragments should be artificially partitioned. 

The molecules in these data-sets were then characterised by the presence or absence of the screens that are used for substructure searching in SOCRATES, the Pfizer Central Research chemical and biological databank system . In the case of the 2-D structures, there were 1315 atom-centred, bond-centred and atom sequence fragment screens in the case of the 3-D structures, there were 1471 inter-atomic distance screens. ... 

It is becoming increasingly apparent that a very extensive chemistry is associated with the dimetal species (1), and (3) - (13). Three types of reaction may be identified (i) aSTdition of other metal ligand fragments, discussed in the next Section, (ii) replacement of peripheral ligands on the metal centres, and (iii) reactions at the bridging carbon atom. One example of (ii) and (iii) will suffice to illustrate the scope and potential for new chemistry. 

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