At the core of the automated prediction of fragmentation and rearrangement pathways is a computer-based system for the extraction of unimolecular decomposition mechanisms from user provided reactions. This complex software system decodes the underlying principle of fragmentation mechanisms from reaction drawings and builds a knowledge base of fragmentation events. This unique system works fully automatically and replaces the need for the tedious manual input of atom-atom correspondence in precursor and product ion pairs. A computer learning procedure has been developed to allow the processing of specific fragmentation details. Similarly, in experimental mechanistic studies, labeled or generic structures can be used to direct the desired dissociation route. By means of deuteria or substituents (R) participation, the decoding algorithm unambiguously extracts the underlying mechanism.

Since many reactions stored in a fragmentation library follow general fragmentation rules, which can be predicted by the use of preprogrammed unimolecular reactions, the library distinguishes between class specific mechanisms and general fragmentation reactions. After a reaction has been saved into the database, the system attempts to identify a general fragmentation rule and assigns the relevant reaction symbol above the arrow. The reaction symbol of every reaction in Fragmentation Library window can be edited by double clicking on the arrow and entering the new formatted text into the annotation dialog box.

As regards fragmentation prediction, the determination of the preferred ionization site is as important as a detailed knowledge of the fragmentation mechanism. The system supports the virtual generation of charged molecules based on library ionization reactions using the exact location of the positive or negative charge, or the unspecified charge location symbol that can be assigned to a structure drawing.

HighChem Fragmentation Library™ and Fragmentation Library™ are trademarks of HighChem, Ltd., Slovak Republic