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*   Understanding Unspecified Charge Sites
Use the Mass Frontier application for processing structures where the charge site is not specified. This kind of molecule representation is important when using ionic structures because the favored ionization site or the explicit charge site during fragmentation reactions is often unclear. You can choose from several ion types in the system.
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To create an ionic structure with an unspecified charge site
Select one of the ion types from the list at the bottom of the Structure Editor.
Every structure with an unspecified charge site has this symbol, , on the upper left part of the structure.
Be aware of potential complications when you use an unspecified charge site with fragment prediction. If you attempt to generate fragments from a structure with an unspecified charge location, the system internally predicts all the relevant combinations of the structures with an explicit charge location. This process significantly slows the calculations and increases the number of predicted fragments. When possible, avoid unspecified charge sites in predicting fragments and mechanisms. For additional information, see Base Page.


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Related Topics:
  Selecting Atoms and Bonds
  Editing Atom Properties
  Editing Bond Properties
  Understanding Unspecified Bond Locations
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