13.1 Mass spectral fragmentation patterns

Mass spectral fragmentation patterns reveal crucial details about molecular structure. They show how compounds break apart during ionization, producing unique "fingerprints" for identification.

Understanding these patterns helps decipher a molecule's components and arrangement. By analyzing ion types, abundances, and fragmentation mechanisms, we can unravel complex structures from mass spectral data.

Molecular and Fragment Ions

Types of Ions in Mass Spectra

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• Molecular ion represents the unfragmented molecule after electron ionization
  • Appears at the highest m/z ratio in the spectrum
  • Provides crucial information about the molecular mass of the compound
• Fragment ions form when molecular ions break apart during the ionization process
  • Result from bond cleavages in the original molecule
  • Provide structural information about the compound
• Radical cations contain an unpaired electron and a positive charge
  • Often form as the initial product of electron ionization
  • Can undergo further fragmentation to produce other ions
• Even-electron ions possess no unpaired electrons
  • Form through the loss of a neutral molecule from a radical cation
  • Generally more stable than radical cations

Significance of Ion Types

• Molecular ion peak helps determine the molecular formula of the compound
  • Absence may indicate an unstable molecule or excessive fragmentation
• Fragment ion patterns serve as a "fingerprint" for identifying compounds
  • Specific fragmentation patterns correlate with certain functional groups
• Radical cations often appear as molecular ions in the spectrum
  • Their fragmentation pathways provide insights into molecular structure
• Even-electron ions frequently form abundant peaks in mass spectra
  • Their stability contributes to characteristic fragmentation patterns

Ion Abundance and Stability

Key Spectral Features

• Base peak represents the most intense peak in the mass spectrum
  • Assigned an arbitrary abundance of 100%
  • Other peak intensities reported as a percentage relative to the base peak
• Metastable ions form when ions decompose in the flight tube
  • Appear as broad, diffuse peaks in the spectrum
  • Provide information about fragmentation processes occurring after initial ionization
• Isotope peaks result from the presence of naturally occurring isotopes
  • Appear at higher m/z values than the monoisotopic peak
  • Intensity pattern depends on the elemental composition of the molecule

Factors Affecting Ion Abundance

• Structural features influence the stability and abundance of ions
  • Conjugated systems often produce stable molecular ions
  • Highly branched molecules tend to fragment more readily
• Ionization energy affects the degree of fragmentation
  • Higher energies lead to more extensive fragmentation
  • Lower energies may preserve the molecular ion
• Bond strengths determine which fragments form preferentially
  • Weaker bonds break more easily, producing characteristic fragments
• Rearrangement reactions can stabilize certain ions
  • May lead to unexpected fragment ions in the spectrum

Fragmentation Mechanisms

Common Fragmentation Pathways

• McLafferty rearrangement involves a six-membered transition state
  • Occurs in compounds with a gamma hydrogen relative to a carbonyl group
  • Results in the transfer of a gamma hydrogen to the carbonyl oxygen
  • Produces a characteristic fragment ion with a mass 60 units less than the molecular ion (ketones)
• Alpha cleavage breaks the bond adjacent to a functional group
  • Common in aldehydes, ketones, and other carbonyl compounds
  • Produces fragments that retain the functional group
  • Often results in prominent peaks in the mass spectrum
• Neutral loss involves the elimination of a small, stable molecule
  • Common neutral losses include water, carbon monoxide, and hydrogen gas
  • Produces fragment ions with predictable mass differences from the precursor ion

Structural Information from Fragmentation

• Fragmentation patterns provide clues about functional groups present in the molecule
  • Carbonyl compounds often show McLafferty rearrangement and alpha cleavage
  • Alcohols frequently exhibit loss of water (18 mass units)
• Sequential fragmentation can reveal the carbon skeleton of the molecule
  • Loss of alkyl groups (CnH2n+1) indicates branching points
  • Stepwise loss of 14 mass units (CH2) suggests a straight-chain hydrocarbon
• Characteristic neutral losses help identify specific functional groups
  • Loss of 28 mass units may indicate CO (aldehydes, ketones) or C2H4 (alkenes)
  • Loss of 42 mass units often corresponds to loss of C3H6 (propene) from branched alkanes