13.4 Mass Spectrometry: Molecular Ion, Base Peak, Metastable Peak and McLafferty Rearrangement

13.4.1 How a mass spectrum forms ★★

In electron impact (EI) a 70 eV electron knocks one electron out of the molecule: the molecular ion M⁺•, a radical cation. It carries far more energy than any bond needs, so part of it breaks into fragments. Only charged species are accelerated, sorted by m/z and detected; neutral radicals and molecules are lost unseen.SN

• Molecular (parent) peak: M⁺•, gives the molecular mass. Base peak: the tallest peak, set to 100 %; the most stable ion, often a fragment. Fragment (daughter) ions: everything else. Metastable peak: broad, weak, at a non-integral m/z (13.4.4).SN

13.4.2 The molecular ion ★★

• Nitrogen rule: an odd molecular mass means an odd number of N atoms. Fragments: an even-electron ion containing no N has odd m/z (43, 57, 91, 105); an odd-electron ion with no N has even m/z (58, 60, 74, 92, 120): an even fragment from an odd-electron parent with no N signals a rearrangement, not a simple cleavage.SN
• Where ionisation starts: the electron is removed from the orbital of lowest ionisation energy, n(N) < n(O) ≈ π < σ. In doxepin the N lone pair ionises first CSE 2023 Q8(a)(i) 10m.
• How strong M⁺• is: aromatics, conjugated alkenes, cyclic compounds strong; ketones, amines, esters medium; branched alkanes and alcohols weak or absent (alcohols show M − 18 instead).
• When M⁺• is missing, a peak 15 (CH₃), 18 (H₂O), 29 (C₂H₅ or CHO), 31 (OCH₃) or 45 (OC₂H₅) units above the highest peak is the clue.

13.4.3 Isotope peaks ★★

• ³⁵Cl : ³⁷Cl ≈ 3 : 1, ⁷⁹Br : ⁸¹Br ≈ 1 : 1, so one Cl gives M : M+2 ≈ 3 : 1, one Br ≈ 1 : 1, one Cl + one Br ≈ 3 : 4 : 1, from (3 + x)(1 + x) = 3 + 4x + x² IFoS 2024 Q5(g) 5m.SN
• M+1 from carbon: ¹³C is 1.1 %, so I(M+1)/I(M) ≈ 1.1 % × number of C. A 6.6 % M+1 means about six carbons. S (³⁴S, 4.4 %) also gives a small M+2.SN

13.4.4 Metastable peaks ★★

An ion m₁⁺ that decomposes to m₂⁺ after leaving the source but before the magnet is recorded neither at m₁ nor at m₂ but at a broad, weak peak m*. It proves that m₂ forms from m₁ in one step.

• Doxepin, M⁺• 279 → CH₂=N⁺(CH₃)₂ 58: m* = 58²/279 = 12.06 CSE 2023 Q8(a)(i).SN
• Peaks 106, P, 65, 46.42, 29, 15: 46.42 is the metastable, so P = 65²/46.42 = 91.0; the step 91 → 65 is loss of C₂H₂ (26) from tropylium IFoS 2023 Q5(g) 5m.SN