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*   Features
The Fragments & Mechanisms module uses a mathematical approach to simulating unimolecular ion-decomposition reactions. For additional information, see Previewing Unimolecular Reactions.
The system, which generates possible fragmentation and rearrangement pathways, is based on these assumptions:
The system optionally predicts reaction pathways that are based on general fragmentation and rearrangement rules. This feature does not include compound-specific mechanisms that cannot be applied generally. At first, this might seem to be a disadvantage; however, you can use this feature in combination with a substructure search for identifying specific compound classes. For additional information, see Unexplained Peaks.
The system optionally accesses an intelligent fragmentation mechanism knowledge base for predicting unimolecular decomposition reactions. HighChem Fragmentation Library currently contains approximately 19 000 individual mechanisms. You can also include your own mechanisms in fragmentation prediction. For additional information, see Base Page, Fragmentation Library , or Using Library Reactions in Fragmentation Prediction.
Every ion-decomposition reaction that is generated is based on the charge localization concept. The application determines exactly where the charge site in all precursor and product ions is located. The system internally generates resonance reactions, which are not displayed by default. For additional information, see Resonance Page.
These reactions can move charge sites to distant locations and, in some complicated structures, the charge localization concept might appear to have been violated. If a reaction step is not clear, you can set up the system to display mechanisms along with resonance reactions. You can, however, use an unspecified charge location that is internally transformed to all combinatorial structures with a localized charge.
The Mass Frontier application generates only unimolecular reactions. The reaction pathways are displayed as linear reaction mechanisms, which incorporate one intermediate site on the left and one intermediate site on the right for each reaction step. The application includes only ionic products in reaction pathways; it does not display neutral fragments.
The application generates reaction mechanisms in accordance with the Even-Electron rule. The Even-Electron rule says that the homolytic bond cleavages of an even electron ion are energetically unfavorable. This means that the application never generates radical cations from an even-electron ion.
Using the General fragmentation and rearrangement rules option, the application can only generate fragments from bond cleavages. It does not support bond creation, except creation of an H-X bond (X = any element) in hydrogen rearrangements. For this option, the system does not include ring contractions, cyclizations, or skeletal and non-hydrogen rearrangements. The Fragmentation Library option supports bond creation with all rearrangements and ring transformations. For additional information, see H-Rearrangements Page or Fragmentation Library.
The application supports electron impact, protonation, deprotonation, cluster ion formation, alkali metal adducts, and chemical ionization methods.
The mechanisms generated by the Mass Frontier application contain formally possible reaction steps. The system does not determine the stability of product ions from thermodynamic data or rates of reaction. When evaluating generated mechanisms, keep this rule in mind: Short and uncomplicated reaction pathways are more favorable than complex mechanisms involving complicated, multistep hydrogen rearrangements.

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Related Topics:
  Generating Fragments and Mechanisms
  Using the Fragments & Mechanisms Window
  Previewing Unimolecular Reactions
  Generating Fragments for Multiple Structures
  Specifying Reaction Restrictions
  Working with Generated Fragments
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