Mass Frontier allows the processing of structures where the charge site is not specified. This kind of molecule representation is of great importance when dealing with ionic structures, since the favored ionization site or the explicit charge site during fragmentation reactions is often unclear. Several ion types can be chosen in the program.

To create an ionic structure with an unspecified charge site, select one of the ion types from the combo box at the bottom of Structure Editor. Every structure with an unspecified charge site has a specific symbol  on the upper left part of the structure.

Note: It is very convenient to use an unspecified charge site, but there are some potential complications if this is used in connection with fragment prediction. If you attempt to generate fragments from a structure with an unspecified charge location, the program will internally predict all the relevant combinations of the structures with an explicit charge location. This will significantly slow the calculations and dramatically increase the number of predicted fragments. We strongly advise you to avoid unspecified charge sites in the prediction of fragments and mechanisms, if at all possible.