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*   Understanding Unspecified Bond Locations
Mass spectrometry cannot always provide information about the exact position of a functional group on a chain or ring portion of a structure. In several application areas, however, even incompletely characterized molecules can be sufficient to study a particular phenomenon. A typical example is metabolite characterization in an early drug discovery process where knowing the precise location of the site of biotransformation action is of little importance.
For displaying and calculating the monoisotopic mass or the isotopic pattern of a fragment or molecule with an unspecified bond location (see Isotope Pattern), use the Ellipse tool, . The ellipse visually defines the region on a structure where you can potentially attach a functional group. To correctly interpret an unspecified bond location, the ellipse must enclose one or more atoms of the core structure and a single atom of a functional group that is not attached to the core structure.
Note  The Ellipse tool is available only in the Structure Editor module. You cannot use a structure with an unspecified bond location in other Mass Frontier modules. The Mass Frontier application does not support the generation of fragments and mechanisms from such structures.


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