Library reactions create a database of fragmentation and rearrangement mechanisms that you
can apply to your structures to predict the fragmentation pathways occurring in a mass spectrometer. The library mechanisms are extensions to the general fragmentation rules, which might not cover all the complex processes for a broad spectrum of ionization and ion activation techniques. For additional information, see Previewing Unimolecular Reactions
Library mechanisms provide flexibility in altering predicted fragmentation pathways and
entering highly specific mechanisms that apply to a limited class of compounds. Because the Mass Frontier application contains approximately 130 000 reactions, the fragmentation predictability is much higher than if only general rules were applied. This is particularly true for low energetic experiments such as ESI or APCI that often yield complicated skeletal and hydrogen rearrangements, unusual ring closures, or complex fragmentations.
Any recognized and active mechanism that has been saved into a library serves as a knowledge
base for predicting fragmentation pathways. After drawing and saving a reaction into any fragmentation library, you can use the mechanism template for predicting fragmentation pathways for any structure to which the derived mechanism can be applied. The applicability range depends on many factors, but structurally similar compounds with a common ring scaffold usually exhibit identical fragmentation mechanisms.
Fragment stability and general ion energetics depend on many thermodynamical parameters,
and even a slight structural dissimilarity between two molecules can result in large differences in the course of fragmentation pathways. For example, two identical structures with a simple hydroxy group difference can occasionally exhibit completely different spectra and the derived fragmentation analogy based on library reactions might not always reflect the real fragmentation events for structural analogs.
When a fragmentation reaction is predicted using a library reaction, you can double-click the
Lib arrow label to see the corresponding mechanism. Both template and generated fragmentation mechanisms are displayed in red in the Fragmentation view and in the Fragments & Mechanisms window. See Generated fragmentation mechanisms