Fragmentation

Molecular ions are often unstable and break apart in the mass spectrometer. This is fragmentation. A molecular ion splits into a positive ion and a neutral radical:M⁺ → X⁺ + Y•Only the positive ion, X⁺, is detected. The radical has no charge, so it is not detected, but you can work out what was lost from the difference between the m/z of M⁺ and the fragment.Common fragment ions (m/z)
• 15: CH₃⁺
• 29: C₂H₅⁺
• 31: CH₂OH⁺
• 43: C₃H₇⁺ or CH₃CO⁺
• 45: COOH⁺Common losses from M⁺
• M − 15: loss of CH₃• (a methyl radical)
• M − 17: loss of OH•
• M − 29: loss of C₂H₅•Fragments show which groups of atoms are joined together, so they can distinguish isomers that have the same M_r.Worked example: propan-1-ol and propan-2-ol both have M_r = 60.
• Propan-1-ol, CH₃CH₂CH₂OH, gives a large peak at m/z 31 (12 + 2 + 16 + 1 = 31), from CH₂OH⁺: CH₃CH₂CH₂OH⁺ → CH₂OH⁺ + C₂H₅•.
• Propan-2-ol, CH₃CH(OH)CH₃, gives a large peak at m/z 45 (60 − 15), from loss of a methyl radical to form CH₃CHOH⁺.