17.4 Identification of a Molecule by Fragmentation Pattern

Mass spectrometry does more than measure molecular mass — the fragmentation pattern (the collection of fragment peaks) acts as a unique fingerprint that allows identification of organic molecules.

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The Molecular Ion Peak ($M^{+}$)

When a molecule enters the mass spectrometer, it is bombarded by high-energy electrons (typically 70 eV), causing it to lose one electron:

$M+e^{-}\to M^{+\bullet }+2e^{-}$

The resulting species, $M^{+\bullet }$ (a radical cation), is called the molecular ion. Its $m/z$ value equals the relative molecular mass ($M_r$) of the compound — this is the key to deducing molecular mass from a mass spectrum.

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Fragmentation

The molecular ion is often unstable and breaks apart — this is called fragmentation:

$M^{+\bullet }\to {\text{fragment cation}}^{+}+{\text{neutral radical}}^{\bullet }$

• Only the positively charged fragment ions are detected (neutral radicals carry no charge and are lost in the vacuum).
• The collection of fragment peaks at various $m/z$ values forms the fragmentation pattern.
• Each fragment peak corresponds to a specific structural unit of the molecule.

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The Base Peak

The base peak is the most intense (tallest) peak in the mass spectrum. It represents the most stable and most abundant fragment ion. By convention, it is assigned a relative abundance of 100%, and all other peaks are measured relative to it.

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Deducing Molecular Mass from the $M^{+}$ Peak

The $m/z$ value of the molecular ion peak directly gives $M_r$:

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Characteristic Fragment Ions

Certain structural groups produce characteristic fragment ions at predictable $m/z$ values. Recognising these allows identification of functional groups:

Alpha ($\alpha$) Cleavage

Fragmentation preferentially occurs at the bond adjacent (alpha) to a functional group, because the resulting cation is stabilised by resonance or inductive effects.

Example — Methyl ketones: $C{H}_3-CO-R\to [C{H}_{3}CO{]}^{+}+R^{\bullet }$ The acylium ion $[C{H}_{3}CO{]}^{+}$ at $m/z=43$ is characteristic of all methyl ketones.

Example — Propan-2-ol ($M_r=60$): $C{H}_{3}CH(OH)C{H}_3^{+\bullet }\to [C{H}_{3}CHOH{]}^{+}+C{H}_3^{\bullet }$ Loss of $C{H}_3$ (mass 15) gives a fragment at $m/z=45$.

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Fragmentation and Neutral Species

Only cations are detected. When a molecular ion fragments:

• The cation ($m/z$ recorded) → detected
• The neutral radical → NOT detected (no charge, lost in vacuum)

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Isotope Peaks: $M+1$ and $M+2$

Small peaks appear at $m/z=M+1$ and $m/z=M+2$ due to naturally occurring heavier isotopes.

$M+2$ Peak — Identifying Halogens

Halogens with two abundant isotopes produce a distinctive double peak pattern:

• A 3:1 ratio of $M$ to $M+2$ peaks → chlorine present
• A 1:1 ratio of $M$ to $M+2$ peaks → bromine present

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Summary: Using Fragmentation Patterns for Identification

1. Find $M^{+}$ peak → gives $M_r$ of the molecule
2. Check $M+2$ peak ratio → identifies Cl (3:1) or Br (1:1)
3. Identify base peak → most stable fragment, often indicates functional group
4. Calculate mass differences between $M^{+}$ and fragment peaks → identifies groups lost
5. Match characteristic fragments (e.g., $m/z=43$ for $C{H}_{3}C{O}^{+}$) → confirms functional groups