Mass Frontier’s expert system automatically extracts fragmentation mechanisms from a reaction drawing after a scheme has been saved. If a reaction follows one of the pre-programmed general fragmentation rules, the arrow will be captioned with the particular rule abbreviation.

Even if a reaction is formally correct, it may not be possible to derive a reaction mechanism from a user provided drawing. This can occur if the user enters an unfeasible fragmentation mechanism or because the unimolecular reaction is incomprehensible to the expert system. If a mechanism cannot be extracted, the reaction arrow will have a cross through it. In this case, the mechanism is reduced to the exact precursor and product structures and only the identical neutral or ionic precursor is matched with the user provided structure in the fragmentation prediction process.

The software will sometimes be able to decode a mechanism from a drawn reaction but the atom-matching procedure will be unable to find the corresponding atom counterparts on both sides of the reaction leading to partially recognized mechanisms. When this occurs, the reaction arrow will appear with a small line through it at right angles. This kind of reaction can only be used for fragment prediction for some input structures according to the fragmentation algorithms decision. So do not be surprised if a partially recognized reaction mechanism is not selected for fragments prediction, even when your input fragment looks similar to the precursor in the library reaction.

To overcome such a problem with unrecognized or partially recognized mechanisms, we recommend trying to decompose complex one-step mechanisms into a number of simple reaction steps and then save these in a fragmentation library.

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