Mass Fragmentation Tool

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The Mass Fragmentation tool allows you to break existing structures across one or more bonds. This mimics the molecular fragmentation in a mass spectrometer, but does not have any predictive qualities: you must specify what bonds are to be broken.

To fragment a structure:

1. Drag the mouse across one or more bonds.

A line is drawn across the bonds that disappears when you release the mouse button. No bonds are visibly broken until the mouse is released. When the mouse is released, any bonds crossed by the line are broken

2. If you want to indicate which bonds will be broken without actually breaking them, hit the Option key after drawing the line.

3. The Option key also allows you to "turn corners" and cut more than one bond.

When the line crosses a bond, the formula and exact mass for the fragments on either side of the bond are displayed as if the bond were homolytically broken. That is, a single bond turns into a monoradical on each fragment; a double bonds turns into a pair of diradicals. If more than one bond is crossed, all fragments on each side of the line are considered together. If the only bond crossed is a ring bond, a single formula/mass pair is displayed.

NOTE: It is possible to draw lines that tie themselves in knots. Use this tool with caution to avoid unrealistic fragmentation.

You can reposition the formula and mass displays (they are text objects), or delete them altogether.