Mass spectrometry is a powerful tool for identifying organic compounds. It works by ionizing molecules and analyzing their fragmentation patterns. Different functional groups produce unique mass spectra, allowing chemists to determine molecular structures and compositions.

Understanding mass spectrometry helps you decode the molecular puzzle. By recognizing characteristic peaks and fragmentation patterns, you can identify functional groups, determine molecular masses, and piece together structural information about unknown compounds.

Mass Spectrometry of Common Functional Groups

Ionization and Detection Methods

• Electron impact (EI): High-energy electrons collide with sample molecules, causing ionization and fragmentation
• Chemical ionization (CI): Softer ionization technique that produces less fragmentation
• Mass-to-charge ratio (m/z): Measurement used to identify ions based on their mass and charge
• Base peak: Most intense peak in the mass spectrum, representing the most stable fragment ion

Fragmentation patterns of organic compounds

• Alcohols
  • Molecular ion peak ($M^+$) usually present but may have low intensity due to easy fragmentation
  • $[M-OH]^+$ peak formed by loss of hydroxyl group (ethanol)
  • $[M-H_2O]^+$ peak formed by loss of water molecule via rearrangement (propanol)
• Amines
  • Molecular ion peak ($M^+$) usually present and relatively stable compared to alcohols
  • $[M-1]^+$ peak formed by loss of hydrogen atom from nitrogen (methylamine)
  • $[M-CH_2NH_2]^+$ peak formed by $\alpha$-cleavage adjacent to nitrogen atom (ethylamine)
• Halides
  • Molecular ion peak ($M^+$) usually present with characteristic isotope patterns
    • Chlorine: $M^+$ and $[M+2]^+$ peaks in 3:1 ratio due to $^{35}Cl$ and $^{37}Cl$ isotopes (chloroethane)
    • Bromine: $M^+$ and $[M+2]^+$ peaks in 1:1 ratio due to $^{79}Br$ and $^{81}Br$ isotopes (bromoethane)
  • $[M-X]^+$ peak formed by loss of halogen atom X (X = F, Cl, Br, I) (iodoethane)
• Carbonyl compounds (aldehydes and ketones)
  • Molecular ion peak ($M^+$) usually present but may have low intensity due to easy fragmentation
  • $[M-CO]^+$ peak formed by loss of carbon monoxide (acetone)
  • $\alpha$-cleavage peaks on either side of the carbonyl group (propanal)
  • McLafferty rearrangement peak for aldehydes and ketones with $\gamma$-hydrogen (2-pentanone)

Mass spectra for structural determination

• Determine molecular mass from the molecular ion peak ($M^+$) (butanal: 72)
• Identify functional groups based on characteristic fragmentation patterns
  • Alcohols: $[M-OH]^+$ and $[M-H_2O]^+$ peaks (ethanol: 31 and 45)
  • Amines: $[M-1]^+$ and $[M-CH_2NH_2]^+$ peaks (propylamine: 59 and 30)
  • Halides: Characteristic isotope patterns and $[M-X]^+$ peaks (chlorobutane: 92 and 57)
  • Carbonyl compounds: $[M-CO]^+$ and $\alpha$-cleavage peaks (2-butanone: 57 and 43, 29)
• Analyze relative abundance of fragment ions to determine most stable and dominant fragments
• Use fragmentation patterns and mass differences between peaks to propose molecular structure
• Parent peak: Represents the molecular ion and provides information about the compound's molecular weight

Nitrogen rule in molecular analysis

• Nitrogen rule: odd number of nitrogen atoms $\rightarrow$ odd nominal mass, zero or even number of nitrogen atoms $\rightarrow$ even nominal mass
• Determine nominal mass from molecular ion peak ($M^+$)
  1. Odd nominal mass indicates odd number of nitrogen atoms (1, 3, 5, etc.) (pyridine: 79)
  2. Even nominal mass indicates zero or even number of nitrogen atoms (0, 2, 4, etc.) (aniline: 93)
• Use presence or absence of nitrogen atoms with other fragmentation patterns to propose molecular structure (4-aminobutanoic acid: 103, odd nominal mass, amine fragments)