LIGAND, computer program

Fabiato, A. (1988). Computer programs for calculating total from specified free or free from specified total ionic concentrations in aqueous solutions containing multiple metals and ligands. Method. Enzymol. 157 378-417. 

Finally, it could be asked why it is so important to properly identify stereogenic centers and prefer them to helical units The main practical reason is that most molecules, when realistically described, e.g., by a crystal structure, contain numerous helical units and it is exceedingly difficult, particularly with a computer program, to sort out those that are invariant to physical conditions (see Section 1.1.1.). In general, it is advisable to base specification of stereogenic units on constitutional or configurational distinctions of ligands, as these are normally less affected by external conditions than conformational properties. 

The basis of molecular modeling is that all important molecular properties, i. e., stabilities, reactivities and electronic properties, are related to the molecular structure (Fig. 1.1). Therefore, if it is possible to develop algorithms that are able to calculate a structure with a given stoichiometry and connectivity, it must be possible to compute the molecular properties based on the calculated structure, and vice versa. There are many different approaches and related computer programs, including ab-initio calculations, various semi-empirical molecular orbital (MO) methods, ligand field calculations, molecular mechanics, purely geometrical approaches, and neural networks, that can calculate structures and one or more additional molecular properties. 

Analysis of the various equilibria by a curve-fitting computer program (such as Hyperquad) along with knowledge of the ligand s p KA allows the determination of the amount of uncomplexed ligand and hence the concentration of the complex and the stability constants for the metal complexation reaction, Scheme 1.1... 

Figure 1 depicts a molecular view of [PdPh (R)-(BINAP) ]+ species which was drawn with the Chem 3D computer program using the partial X-ray structure of [PdCl2 (R)-BINAP ]. It is seen that the lower part of the empty coordination site widely opens whereas the upper part is blocked by one of the phenyl groups of the BINAP ligand. 

Binding parameters are calculated from computer programs, one example being the ligand program of... 

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