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Autofragmentation
Once a structure has been drawn or read from file into MSC Pro, you can choose Autofragment to automatically generate a list of all possible fragments that can be formed from the structure by the breaking of bonds taken one or two at a time. Autofragment is accessed as a selection from the Main menu, or by simply clicking on the Speedbutton with the image of a hammer on it. Autofragment is only available when Analyze mode is active which can be selected with the option button at the lower left of the main Structure window or by pressing F3. The current state of MSC, either Draw or Fragment, is indicated by the state of the selection buttons on the lower left in which one always will be down, and also by the label reading either "Draw" or "Fragment" located just to right of the Toolbar at the top of the window.
You can select to form only single break fragments, or fragments arising from both one and two bond breakages, by selecting the appropriate option on the Autofragment window. You can also choose to mark all potential odd-electron ions in the resulting list by clicking on the Mark OE Ions box. In the latter case, all resulting odd-electron fragments will be marked with a dot-plus symbol. Both two-bond breaks and Mark OE ions are pre-selected by default, but can be changed if desired.
Autofragmentation can be used with compounds having molecular weights in excess of 1,000 amu; however, it is possible to exceed the capacity of this routine when extremely large structures are analyzed. If that should occur, a popup box will appear indicating that the structure is too large to autofragment. This should rarely be encountered, and manual fragmentations would still be possible, of course.
Following an autofragmentation, the resulting fragments will be sorted and all unique fragments will be displayed in a list on screen. A fragment is unique when it consists of one specific elemental composition. Thus, some masses may be included multiple times in the list, but each entry will represent one unique substructure in the molecule. You can click on any mass in the list to highlight the corresponding substructure on the molecule. Click the 'Isotopes' button to display the isotopic profile for the currently selected fragment.
Evaluate' will display a list of possible ions or losses based on the current structure. Unlike the main list which is comprehensive, the Evaluate results are restricted to more likely fragments, and may also include certain rearrangement ions such as McLafferty products and tropylium ions, etc. If you prefer to always show both the complete Autofragmentation list and the Evaluate results windows simultaneously by default, then click on the "Always Display Evaluate Window" option box on page 2 in Preferences and click Save.
Clicking on the Print button will print a summary list including each mass present, and the number of unique fragments contributing to that mass. Clicking the Compare Spectrum button will open the Spectrum window to allow comparisons with a selected mass spectrum. See the Match topic for more information on this. Select 'Exit' to close the AutoFragmentation window and return to the main screen.