Key Mass Spectrometry Fragmentation Patterns to Know for Spectroscopy

Mass spectrometry fragmentation patterns reveal how molecules break apart, providing insights into their structure and composition. Key peaks like the molecular ion and base peak help identify the intact molecule and its most stable fragments, guiding analysis in spectroscopy.

1. Molecular ion peak

   • Represents the intact molecule's mass in the mass spectrum.
   • Indicates the molecular weight of the compound being analyzed.
   • Often appears as the highest m/z value in the spectrum, unless there are significant fragmentations.

2. Base peak

   • The most intense peak in the mass spectrum, representing the most stable ion.
   • Serves as a reference point for comparing the intensities of other peaks.
   • May not correspond to the molecular ion, highlighting common fragmentation pathways.

3. Isotope peaks

   • Result from the presence of isotopes of elements in the molecule (e.g., ^13C, ^15N).
   • Typically appear as small peaks adjacent to the molecular ion peak.
   • Help in determining the elemental composition of the compound.

4. M+1 and M+2 peaks

   • M+1 peak indicates the presence of one isotope (e.g., ^13C) in the molecular ion.
   • M+2 peak arises from the presence of two isotopes (e.g., ^13C and ^18O).
   • The ratio of these peaks can provide insights into the number of specific isotopes in the molecule.

5. Alpha cleavage

   • A fragmentation process where a bond adjacent to a functional group breaks.
   • Often leads to the formation of a stable ion and a neutral fragment.
   • Common in carbonyl compounds and can help identify functional groups.

6. McLafferty rearrangement

   • A specific fragmentation pathway involving the transfer of a hydrogen atom.
   • Typically occurs in compounds with a carbonyl group and an allylic hydrogen.
   • Results in the formation of a stable ion and a smaller fragment, aiding in structural elucidation.

7. Benzyl cleavage

   • Involves the cleavage of the bond between a benzyl group and the rest of the molecule.
   • Common in aromatic compounds, leading to the formation of a stable benzyl cation.
   • Useful for identifying the presence of benzyl substituents in the structure.

8. Retro-Diels-Alder fragmentation

   • A fragmentation reaction that reverses the Diels-Alder reaction.
   • Typically occurs in cyclic compounds, leading to the formation of smaller fragments.
   • Helps in understanding the structure of complex cyclic molecules.

9. Loss of water (M-18)

   • A common fragmentation pathway where a water molecule is lost from the molecular ion.
   • Frequently observed in alcohols, acids, and other functional groups containing hydroxyls.
   • Indicates the presence of hydroxyl groups in the original structure.

10. Loss of carbon monoxide (M-28)

    • Involves the elimination of carbon monoxide from the molecular ion.
    • Often seen in compounds with carbonyl groups or in certain aromatic systems.
    • Can provide clues about the presence of specific functional groups.

11. Nitrogen rule

    • States that compounds with an odd number of nitrogen atoms will have an odd molecular ion.
    • Conversely, compounds with an even number of nitrogen atoms will have an even molecular ion.
    • A useful rule for predicting the molecular ion's parity and aiding in structural analysis.

12. Even-electron rule

    • Suggests that stable ions tend to have an even number of electrons.
    • Fragmentation patterns often favor the formation of even-electron ions.
    • Helps in predicting the stability and likelihood of certain fragmentation pathways.

13. Tropylium ion formation

    • Involves the formation of a stable tropylium ion (C7H7+) from aromatic compounds.
    • Characterized by a resonance-stabilized cation, contributing to its stability.
    • Commonly observed in the fragmentation of toluene and related compounds.

14. Aromatic stabilization

    • Refers to the stability conferred by aromaticity in cyclic compounds.
    • Aromatic systems often resist fragmentation due to their stable electronic structure.
    • Can influence the fragmentation pathways and the types of ions formed.

15. Alkyl chain fragmentation

    • Involves the cleavage of carbon-carbon bonds in alkyl chains.
    • Results in the formation of smaller alkyl cations and neutral fragments.
    • Provides information about the length and branching of alkyl chains in the molecule.