MASS SPECTROMETRY: UNDERSTANDING
RADICALS, IONS, AND PROTONATION
(MH⁺)
1. WHAT IS A RADICAL?
A radical (also known as a free radical) is any atom, molecule, or ion that contains at
least one unpaired electron in its outermost shell.
Key Features:
•
•
•
Unpaired electron: Makes radicals highly reactive.
Notation: A dot (·) is used to indicate the unpaired electron. For example: Cl·, OH·,
CH₃·.
Charge: Radicals can be neutral or charged.
Examples:
•
•
•
Cl·: A chlorine radical with 7 valence electrons (1 unpaired).
OH·: Hydroxyl radical.
O₂⁻·: A radical anion with both a negative charge and an unpaired electron.
2. WHAT IS AN ION?
An ion is an atom or molecule that has a net electrical charge due to the gain or loss of
one or more electrons.
Types of Ions:
•
Cations: Positively charged ions (e.g. Na⁺, NH₄⁺).
•
Anions: Negatively charged ions (e.g. Cl⁻, OH⁻).
Key Features:
•
•
All electrons may be paired — having a charge does not mean the species is a
radical.
Stable ions often have complete valence shells (octet or duet rule).
Examples:
•
•
Cl⁻: Has 8 valence electrons (complete octet, all paired) → stable anion.
Na⁺: Lost one electron to become a cation → all remaining electrons are paired.
3. RELATIONSHIP BETWEEN RADICALS AND IONS
Category
Radicals
Ions
Radical Ions
Neutral Radicals
Even-Electron
Ions
Description
Species with at least one unpaired electron. May be neutral or
charged.
Species with a net charge due to gain or loss of electrons.
Species that are both radicals and ions. Example: CH₄⁺·, O₂⁻·
No charge, but has unpaired electron. Example: NO, Cl·
Charged species with all electrons paired. Example: NH₄⁺, Cl⁻
4. COMMON MISUNDERSTANDING: DO ALL GAINED
ELECTRONS CREATE RADICALS?
No, adding or removing electrons does not automatically create radicals. It depends on
whether an unpaired electron remains after the process.
Clarification with Examples:
1. Chlorine Atom Gains 1 Electron
a. Cl (7 valence electrons) + e⁻ → Cl⁻ (8 electrons)
b. Now all electrons are paired → not a radical, just an ion.
2. Chlorine Atom by Itself
a. Cl· has 7 electrons → 1 unpaired → radical, no charge.
3. O₂ + e⁻ → O₂⁻·
a. Gains 1 electron, resulting in one unpaired electron → radical anion (charged
+ radical)
4. NO (Nitric Oxide)
a. 11 total valence electrons → unpaired electron present → neutral radical
5. CH₄⁺· (from mass spectrometry)
a. Lost one electron, leaving unpaired electron → radical cation
5. RADICALS IN MASS SPECTROMETRY (EI)
In Electron Ionization (EI):
•
•
A high-energy electron collides with the molecule (M) and removes one of its
electrons.
The result is a radical cation, denoted M⁺·.
Reaction:
M + e⁻ → M⁺· + 2e⁻
•
M⁺· is the molecular ion (also called the parent ion).
•
M⁺· often fragments into:
o Even-electron cations → detected
o Neutral radicals → not detected (no charge)
Example:
Methanol (CH₃OH) in EI:
•
Molecular ion formed: CH₃OH⁺· (m/z = 32)
6. CHEMICAL IONIZATION (CI) AND PROTONATION
Chemical Ionization is a softer ionization technique compared to EI. It adds a proton (H⁺)
instead of removing an electron.
Mechanism:
1. A reagent gas (like methane, NH₃, or isobutane) is introduced.
2. The gas is ionized to produce proton donors such as CH₅⁺ or NH₄⁺.
3. These ions transfer a proton (H⁺) to the molecule of interest (M).
General Reaction:
M + H⁺ → MH⁺
•
•
•
MH⁺ is called the protonated molecular ion.
It is not a radical, because the added proton doesn't introduce an unpaired
electron.
The ion is charged (+1), and electrons are still paired.
CI vs EI Summary Table
Feature
Process
Ion formed
Electron pairing
Resulting species
Fragmentation
Spectrum complexity
Molecular weight
identification
Electron Ionization (EI)
Electron is removed
M⁺· (radical cation)
Unpaired electron remains
Radical + Ion
Extensive
High
Can be tricky
(fragmentation)
Example of Protonation in CI:
Methanol (CH₃OH) + CH₅⁺ → CH₃OH₂⁺ + CH₄
Chemical Ionization (CI)
Proton is added
MH⁺ (protonated ion)
All electrons paired
Ion only
Minimal
Low
Easier (stable MH⁺ peak)
•
•
Methanol accepts a proton → becomes CH₃OH₂⁺ (MH⁺)
Detected mass-to-charge ratio (m/z) = 33
•
Protonated molecule is more stable and cleanly observed
7. CHEAT SHEET: HOW TO TELL WHAT YOU'RE LOOKING
AT
Species
Cl·
Cl⁻
CH₄⁺·
NO
O₂⁻·
NH₄⁺
CH₃OH₂⁺
Unpaired Electron?
Yes
No
Yes
Yes
Yes
No
No
Charge?
No
Yes
Yes
No
Yes
Yes
Yes
Radical?
Yes
No
Yes
Yes
Yes
No
No
Ion?
No
Yes
Yes
No
Yes
Yes
Yes
8. FINAL KEY POINTS
1. Radicals are about unpaired electrons, not charge.
2. Ions are about charge, not necessarily unpaired electrons.
3. A species can be:
a. A radical only
b. An ion only
c. A radical ion (has both)
4. In mass spectrometry:
a. Electron Ionization creates radical cations (M⁺·)
b. Chemical Ionization adds a proton to form MH⁺ (even-electron, nonradical ion)
5. CI produces cleaner spectra and helps identify molecular weight easily.
6. Knowing whether a species is a radical or not helps in understanding:
a. Reactivity
b. Spectral peaks
c. Fragmentation behavior