vDatabase of observed biodegradation pathways for 183 chemicals, mainly pesticides was used to build the model. Substances with a variety of chemical functionality, such as acid amides, aniline and nitrobenzenes, dithio and thiolcarbamates, five- and six-rings heterocyclic compounds, phenyl (aryl) carbamates, phosphoro(di)thiolates, sulfonylureas, etc. are presented in the database. Metabolic fate of chemicals is simulated via the principal molecular transformations extracted from the metabolic pathway database. The molecular transformation consists of parent sub-molecular fragment, transformation products and inhibiting functional groups. The hierarchy of the transformations and their probabilities are used to control the propagation of the catabolic maps of the chemicals.