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*   Extracting Mechanisms
The automated prediction of fragmentation and rearrangement pathways extracts unimolecular decomposition mechanisms from reactions you provide. The application decodes the underlying principle of fragmentation mechanisms from reaction drawings and builds a knowledge base of fragmentation events, replacing the need for the manual input of atom-atom correspondence in precursor and product ion pairs. For additional information, see Drawing Fragmentation Reactions or Base Page.
The application processes specific fragmentation details (similar to labeled or generic structures) for use in experimental mechanistic studies to direct the dissociation route. Using deuteria or substituents participation, the decoding algorithm unambiguously extracts the underlying mechanism.
Extracted mechanisms
Because many reactions stored in a fragmentation library follow general fragmentation rules that can be predicted using preprogrammed unimolecular reactions, the library distinguishes between class-specific mechanisms and general fragmentation reactions. After you save a reaction to the database, the application attempts to identify a general fragmentation rule and assigns the relevant reaction symbol above the arrow. You can edit the reaction symbol of every reaction on the Reaction page by double-clicking the arrow and entering the new formatted text into the annotation dialog box.
Note  Reaction symbols do not appear immediately after the reaction is drawn, but only after you save the record in a library. For a description of reaction symbols, see Reaction Symbols.
With respect to fragmentation prediction, determining the preferred ionization site is as important as detailed knowledge of the fragmentation mechanism. The application supports the virtual generation of charged molecules based on library ionization reactions using the exact location of the positive, negative, or unspecified charge location symbol that you can assign to a structure drawing. For additional information about modifying the charge location symbols, see Modifying Atoms and Bonds.
Reaction Symbols
The Mass Frontier application automatically extracts fragmentation mechanisms from a reaction drawing after you save a scheme. When a reaction follows one of the preprogrammed general fragmentation rules, the arrow is labeled with the particular rule abbreviation. For descriptions of these abbreviations, see Reaction Formalism.
Even when a reaction is formally correct, deriving a reaction mechanism from your drawing might not be possible because you entered an unfeasible fragmentation mechanism or the unimolecular reaction is incomprehensible to the application. When a mechanism cannot be extracted, the application puts a cross through the reaction arrow (). 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 your structure in the fragmentation prediction process.
The application can sometimes decode a mechanism from a drawn reaction, but the atom-matching procedure will not be able to find the corresponding atom counterparts on both sides of the reaction leading to partially recognized mechanisms. When this occurs, the reaction arrow appears with a small line through it at right angles. This kind of reaction can be used only for fragment prediction for some input structures according to the decision of the fragmentation algorithm. Even when your input fragment looks similar to the precursor in the library reaction, a partially recognized reaction mechanism might not be selected for fragments prediction.
To overcome such a problem with unrecognized or partially recognized mechanisms, try to decompose complex one-step mechanisms into several simple reaction steps and then save these in a fragmentation library.
Graphical indicators of unrecognized mechanisms


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Related Topics:
  Drawing Fragmentation Reactions
  Editing a Fragmentation Scheme
  Working with Records
  Using Library Reactions in Fragmentation Prediction
  Searching for Fragmentation Criteria
  Comparing Fragments
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