Atom-pair structural fragments

Molecular orbital calculations have also provided theoretical justification for these stereoelectronic effects in tetracovalent and pentacovalent phosphorus species (2-7). As has been shown in molecular orbital calculations on the X -P-X2 (X = 0,N) structural fragments, the X.-P bond is strengthened (as indicated by an increase in the Mulliken overlap population) while the P-X3 bond is weakened when the X atom lone pair is app to the P-X3 bond. Thus, in the g,t conformation of dimethyl phosphate (Structure ll the overlap population for the trans P-0 bond is. 017 electron lower than the overlap population for the gauche P-0 bond. As shown for g,t dimethyl phosphate one lone pair (shaded in 1) on the gauche bond oxygen is app to the trans bond, while no lone pairs on the trans bond oxygen are app to the gauche bond. Thus, the weakest X.-P bond has one app lone pair and no lone pairs on X. app to the P=X2 bond. 1... 

A tremendous number of various fragments are used in structure-property studies atoms, bonds, topological torsions , chains, cycles, atom- and bond-centered fragments, maximum common substructures, line notation (WLN and SMILES) fragments, atom pairs and topological multiplets, substituents and molecular frameworks, basic subgraphs, etc. Their detailed description is given below. 

Two different MACCS keys (or MDL keys) [MACCS keys - MDL Information Systems Inc., 2008 Durant, Leland et al, 2002] are commonly encountered, one containing 960 bits and the other, which is public, containing a subset of 166 bits (ISIS keys). The fragment dictionary is based on a number of atom types, atom pairs, and custom atom environments. There can be a one-to-one relationship between the structural features and bits, or hashing can be used to create a many-to-one or many-to-many relationship between the features and bits. 

Other atoms or fragments have higher connectivities, and hence they form molecules with more atoms combined together by these electron-pairs. Willi more than three atoms bonded in a molecule, we start to have molecules with 3D shapes. When a molecule has many, many atoms, the structural elements become more complex and we may speak about an architecture of a molecule. Figure 1.6 provides a few examples just to illustrate the molecular shapes, which we shall learn during... 

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