Atom type modeling

The most well-known and at the same time the earliest computer model for a molecular structure representation is a wire frame model (Figure 2-123a). This model is also known under other names such as line model or Drciding model [199]. It shows the individual bonds and the angles formed between these bonds. The bonds of a molecule are represented by colored vector lines and the color is derived from the atom type definition. This simple method does not display atoms, but atom positions can be derived from the end and branching points of the wire frame model. In addition, the bond orders between two atoms can be expressed by the number of lines. 

Several models have been published where the fragments are defined on a purely atomic level. This simplifies both the recognition of fragments and the calculation, as correction substructures are not applied (see Eq. (10)). N is the occurrence of the ith atom type. 

Recently, several QSPR solubility prediction models based on a fairly large and diverse data set were generated. Huuskonen developed the models using MLRA and back-propagation neural networks (BPG) on a data set of 1297 diverse compoimds [22]. The compounds were described by 24 atom-type E-state indices and six other topological indices. For the 413 compoimds in the test set, MLRA gave = 0.88 and s = 0.71 and neural network provided... 

If the system can only be modeled feasibly by molecular mechanics, use the potential energy curve-crossing technique or a force held with transition-structure atom types. 

PC Model has some features that are not found in many other molecular mechanics programs. This is one of the few programs that outputs the energy given by the force field and the heat of formation and a strain energy. Atom types for describing transition structures in the MMX force field are included. There is a metal coordination option for setting up calculations with metal atoms. There are also molecular similarity and conformation search functions. 

The crystaHographer assigns more labels and atomic types to more peaks and repeats the refinement. After a few cycles of refinement and assignment of atoms, aH of the atoms, with the possible exception of some hydrogen atoms, are included in the model. 

Carbon has six electrons around the atomic core as shown in Fig. 2. Among them two electrons are in the K-shell being the closest position from the centre of atom, and the residual four electrons in the L-shell. TTie former is the Is state and the latter are divided into two states, 2s and 2p. The chemical bonding between neighbouring carbon atoms is undertaken by the L-shell electrons. Three types of chemical bonds in carbon are single bond contributed from one 2s electron and three 2p electrons to be cited as sp bonding, double bond as sp and triple bond as sp from the hybridised atomic-orbital model. 

Almost all widely used, reliable prediction models for logarithmic partition coefficients, and especially for the octanol-water partition coefficient log P w, are linear regression models with respect to fragment counts, atom types, bond types or... 

I. V. Neural network modeling for estimation of partition coeffident based on atom-type electrotopological state indices. 

---