Electron Ionization and the Molecular Ion
A molecule drifts into a chamber and meets a beam of 70 eV electrons. In about a femtosecond it loses one electron. It becomes a radical cation. Carrying nearly 5 eV of excess internal energy, it often falls apart before a detector ever sees it. This single event, electron ionization (EI), is the workhorse ionization method that built modern mass spectrometry. Understanding why 70 eV is the universal standard is key. So is understanding why the molecular ion is a radical cation rather than a protonated species. And why it sometimes vanishes entirely. These are the keys to reading any EI spectrum correctly. EI matters because it is reproducible in a way few chemical processes are. Any two instruments, on two continents, ionizing the same compound at 70 eV, produce nearly superimposable fragmentation patterns. That reproducibility is what makes the NIST/Wiley spectral libraries searchable. A fingerprint match works only because the ionization physics is standardized down to the electron-volt. Contrast this with ionization-methods-overview softer methods (ESI, MALDI, CI), which preserve the intact molecule. But they sacrifice the rich, comparable fragmentation that lets a chemist deduce structure from first principles. The big picture is thermodynamic and mechanistic at once. Ionization energies (IE) of organic molecules cluster between 7 and 12 eV. Bombarding with 70 eV electrons delivers vastly more energy than needed merely to eject an electron. The surplus is deposited as vibrational energy in the resulting cation. That cation is a genuine radical — it has an odd number of electrons. This odd-electron character, together with the excess internal energy, drives the rich bond-cleavage chemistry explored under interpreting-fragmentation. The molecular ion, M⁺•, is the fossil record of that first ionization event. When it survives long enough to be detected, it anchors the entire spectral interpretation by fixing the molecular weight. This article builds the physical picture of the EI event from electron-impact kinetics. It derives why 70 eV became the de facto standard energy. It works through the appearance-energy/ionization-energy relationship with real numbers. And it gives you the diagnostic rules for finding — or explaining the absence of — M⁺• in a real spectrum. This sets up the fragmentation logic and the GC-MS instrumentation covered elsewhere in this encyclopedia.
- EI bombards gas-phase neutral molecules with ~70 eV electrons, ejecting one electron from the analyte to form M⁺•, an odd-electron radical cation.
- 70 eV is not arbitrary: it sits on the plateau of the ionization efficiency curve, well past threshold, giving reproducible, library-comparable spectra.
- Excess energy above the ionization energy (typically several eV) is deposited as internal (vibrational) energy, driving fragmentation on the microsecond timescale inside the source.
- M⁺• always has an odd number of electrons and, by the nitrogen rule, an odd nominal mass if the molecule contains an odd number of nitrogen atoms (and even otherwise).
- Diagnostic criteria for identifying M⁺•: highest reasonable m/z, plausible losses (no gaps of 4–14 or 21–25 mass units to the next peak), and consistency with the nitrogen rule and isotope pattern.
- Some compounds (heavily branched alcohols, many amines) show vanishing or absent M⁺• because fragmentation is faster than the ion survives to the detector — this is a real limitation, not an instrument fault.
- Key idea: EI ionization energy is fixed at 70 eV because that is where fragmentation becomes reproducible, and the molecular ion is the radical cation M⁺• whose survival — not its formation — is the real analytical challenge.
Where this lives today
GC-MS remains the dominant real-world platform for EI, precisely because gas-phase, thermally stable, volatile analytes are exactly what EI handles best — this pairing is explored fully under gc-ms. Forensic toxicology labs run EI-GC-MS as the confirmatory gold standard for drugs of abuse, because the 70 eV spectrum of, say, cocaine or fentanyl is essentially invariant across instruments and decades, letting a match against a reference library serve as legally admissible identification evidence. Environmental laboratories use EI-GC-MS (EPA Methods 8270, 624, and related) to identify and quantify volatile and semivolatile organic pollutants — PCBs, pesticides, PAHs — again relying on the universality of the 70 eV fragmentation pattern for unambiguous library matching. Petrochemical and flavor/fragrance industries use EI-GC-MS routinely to fingerprint complex hydrocarbon and terpenoid mixtures, exploiting exactly the reproducibility argument developed above: because the ionization physics is fixed, retention time plus EI fragmentation pattern together give near-certain compound identification even in mixtures of hundreds of components. In doping control and sports-anti-doping laboratories, EI-GC-MS after derivatization (to make polar steroid metabolites volatile enough for gas-phase introduction) remains a primary confirmatory technique precisely because its fragmentation is so well characterized and defensible under legal challenge. Modern instrument development continues to refine the classic EI source: "low-energy EI" (operating at 10–20 eV rather than 70 eV) is used specifically to enhance molecular ion survival for structurally fragile analytes, trading spectral-library compatibility for better molecular weight confirmation — a direct, deliberate exploitation of the threshold-vs-plateau physics derived above. Understanding the EI mechanism and the nature of M⁺• is also the essential foundation for reading fragmentation patterns rationally rather than by rote memorization, the subject taken up under interpreting-fragmentation.
Ask the tutor: How do I use the M+1 and M+2 isotope peak intensities to figure out how many carbons, chlorines, or bromines are in my molecular ion?
The physical picture — what actually happens in the source
A sample is volatilized (thermally, or after GC elution) into an evacuated ion source, typically held at 10⁻⁵–10⁻⁶ torr so molecules are effectively isolated in the gas phase — no solvent, no neighboring molecules, no collisional stabilization. A heated filament (rhenium or tungsten, often iridium/thoria coated) emits electrons thermionically. These electrons are accelerated through a potential difference of 70 V and collimated by a weak axial magnetic field (from a permanent magnet flanking the source) into a tight beam that crosses the sample vapor at right angles. When a 70 eV electron passes near a neutral molecule M, three outcomes compete: elastic scattering (no energy transfer), inelastic scattering with excitation but no ionization, and ionization:
The incident electron does not "stick" to the molecule; it knocks a valence electron out via a rapid Coulombic interaction (loosely, the same physics as electron-impact ionization of atoms in a mass spectrometer ion gauge). The process is over on the order of 10⁻¹⁶ s — far faster than any nuclear motion (the Franck–Condon principle applies exactly as it does in electronic spectroscopy: ionization is "vertical," leaving the nuclear framework unchanged at the instant of electron loss). Because ionization removes exactly one electron from a molecule that started with an even number of electrons (essentially all stable neutral organic molecules have closed-shell, even-electron configurations), M⁺• is necessarily a radical cation: it carries a net positive charge and an unpaired electron. This is the single most important structural fact about EI-generated ions, and it governs everything downstream — radical-driven α-cleavages, retro-Diels–Alder fragmentations, McLafferty rearrangements — all of it traces back to the odd-electron bookkeeping fixed at this first step. The incident 70 eV is almost never all converted to ionization energy. Ionization energies (IE) of organic molecules lie mostly in the 7–12 eV range (methane IE = 12.61 eV; benzene IE = 9.24 eV; toluene IE = 8.83 eV; triethylamine IE = 7.50 eV). The difference between 70 eV and the actual IE — typically 55–63 eV — is not simply lost; a variable, statistically distributed fraction is deposited into the internal (vibrational + rotational) energy of the newly formed M⁺•. Because the ionizing electron and the ejected electron together carry away the rest as kinetic energy, the internal energy deposited in M⁺• is broadly distributed, typically peaking a few eV above the IE and tailing out past 10 eV. This spread in internal energies is why EI spectra show a whole population of fragmentation channels rather than one clean pathway — some M⁺• ions have barely enough energy to survive to the detector, others have enough to fragment several times over.
Once formed, M⁺• is accelerated out of the source (typically by 1–10 kV in a magnetic-sector or 2–5 kV in a TOF), and en route to the analyzer it has anywhere from nanoseconds to tens of microseconds to fragment, depending on instrument geometry. Ions that fragment within the source, before extraction, produce the fragment ions that dominate a normal EI spectrum; ions that fragment after acceleration but before the detector, in a sector instrument, can produce diffuse "metastable peaks" at non-integer apparent m/z — a separate diagnostic tool covered under fragmentation interpretation. The ionization efficiency (ions formed per unit path length, per unit pressure) as a function of electron energy is not linear — it rises from an appearance threshold near the IE, climbs steeply, and then plateaus in the 50–100 eV range before slowly declining at much higher energies (Bethe-type behavior, where cross-section eventually falls as electrons pass too quickly for adiabatic interaction). Working near threshold gives poor, energy-sensitive sensitivity and huge run-to-run variability; working on the plateau gives an ionization efficiency that barely changes with small fluctuations in filament emission energy — this stability is precisely why 70 eV, comfortably inside the plateau region for essentially all analytes of interest, was adopted as the field-wide standard.
The core ideas — governing relationships
The energetics of EI rest on three linked quantities: the ionization energy of the neutral, the internal energy deposited in the cation, and the appearance energy of any given fragment ion.
where:
- is the incident electron energy (70 eV in standard EI),
- is the adiabatic or vertical ionization energy of the neutral molecule (eV),
- is the combined kinetic energy carried away by the scattered and ejected electrons,
- is the vibrational/rotational excess energy left in M⁺•, distributed statistically across the ensemble of ionization events.
Reading it: only a fraction of the 70 eV nominally available ever becomes internal energy of the ion; the rest departs as electron kinetic energy. The internal energy distribution, not a single value, is what determines how much (and which) fragmentation occurs — this is why EI spectra show characteristic relative intensities rather than all-or-nothing fragmentation.
where:
- is the appearance energy — the minimum electron energy at which a given fragment ion F⁺ is first observed,
- is the energy required to break the relevant bond(s) from the ground-state M⁺• geometry (often with an activation barrier beyond simple bond dissociation energy, especially for rearrangements),
- the kinetic energy term accounts for any translational energy release partitioned to the departing neutral and ionic fragments.
Reading it: appearance energies are always greater than or equal to the ionization energy of the parent, because you must first form the ion before it can fragment; the difference AE − IE is a direct experimental handle on bond strengths and rearrangement barriers within the ion — this is the basis of energy-resolved mass spectrometry.
where:
- is the nominal (integer, most-abundant-isotope) or monoisotopic mass of the neutral molecule,
- the charge is +1 for essentially all EI molecular ions (multiply charged M²⁺• are vanishingly rare at 70 eV for typical organic analytes),
- so m/z of M⁺• numerically equals the molecular mass — the reason M⁺• is the anchor peak for molecular weight determination.
Reading it: because z = 1 almost always in EI, m/z and mass are numerically interchangeable for the molecular ion — a simplification that does not carry over to ESI, where multiple charging is routine.
Goal. Show quantitatively why choosing an electron energy well above threshold — specifically in the 50–100 eV range — minimizes spectrum-to-spectrum variability, motivating the 70 eV convention.
Step 1 — model the ionization cross-section. Electron-impact ionization cross-sections σ(E) for molecules rise from zero at E = IE, increase roughly linearly just above threshold (Wannier-type near-threshold behavior), pass through a broad maximum typically 3–5× the IE, and then decay slowly (empirically closer to E⁻¹ ln E at high E, per the Bethe formula for inelastic collisions). For a typical organic molecule with IE ≈ 9 eV, the maximum in σ(E) falls near 50–90 eV — this is an empirical regularity found across thousands of measured ionization cross-section curves, not a coincidence tied to any one compound.
Step 2 — quantify sensitivity to small energy drift. Real filaments do not hold electron energy at exactly one value; thermal spread and small potential fluctuations (space-charge effects, contact-potential drift) create an energy spread of order ±1–2 eV around the nominal set point. Define the fractional sensitivity of the ion yield to electron energy as
Near threshold (E close to IE), σ(E) is small and rising steeply, so S(E) is large — a 1 eV drift can change the ion yield by tens of percent. On the plateau (E ≈ 50–100 eV), σ(E) is near its maximum and locally flat, so dσ/dE ≈ 0 and S(E) is small — the same 1 eV drift changes the yield by only a percent or two.
Step 3 — connect to fragmentation reproducibility, not just total ion yield. The internal energy distribution P(E_internal) deposited in M⁺• also broadens and shifts with incident electron energy. Near threshold, P(E_internal) is narrow and close to zero — nearly all M⁺• survive intact (low fragmentation, but also low, energy-sensitive total signal). By 50–70 eV, P(E_internal) has broadened into a stable, reproducible statistical distribution (essentially independent of further increases in E) because the extra energy above threshold is now large compared to typical bond activation energies (3–5 eV), so the pattern of which bonds break, and in what relative proportion, stops changing appreciably with E.
Step 4 — conclude. Both the total ionization efficiency and the internal energy distribution controlling fragmentation become insensitive to small fluctuations in electron energy once E is pushed onto the plateau. 70 eV lies solidly inside this plateau for essentially all IE values encountered in organic and organometallic analytes (IE from ~6 eV for easily ionized amines/aromatics up to ~15 eV for small saturated molecules), which is precisely why the community converged on a single fixed value rather than optimizing per-compound: fixing E at 70 eV trades a small, compound-specific loss in absolute sensitivity for enormous, universal gains in spectral reproducibility, which is what makes spectral-library matching possible at all.
Go deeper · Derivation B · 2 minDeriving the nitrogen rule from valence and parity bookkeeping
Goal. Show why an organic molecule containing an odd number of nitrogen atoms has an odd nominal mass, and why its M⁺• therefore appears at odd m/z — while fragment ions formed by simple bond cleavage flip this parity in a predictable way.
Step 1 — nominal masses and valence of common elements. Using the most abundant isotope for each element (¹H = 1, ¹²C = 12, ¹⁴N = 14, ¹⁶O = 16, ³²S = 32, ³⁵Cl = 35, ⁷⁹Br = 79), notice that C, O, S all have even nominal mass and even valence (4, 2, 2), while H and halogens have odd mass and odd valence (1), and nitrogen is the outlier: nominal mass 14 (even) but valence 3 (odd).
Step 2 — the general parity theorem. For any closed-shell, even-electron neutral molecule built only from H, C, N, O, S, halogens (the overwhelming majority of organic analytes), the nominal molecular mass and the number of nitrogen atoms have linked parities. This follows from the fact that every atom with odd valence must ultimately pair its "extra" bonding capacity with another odd-valence atom or a hydrogen, and tracking the resulting hydrogen count through the degree-of-unsaturation formula shows that the total mass changes parity exactly when the nitrogen count changes parity, because N is simultaneously the only common element with even mass but odd valence — this parity mismatch is what "costs" or "gains" one mass unit relative to an all-even-valence skeleton.
Step 3 — worked parity check with a concrete molecule. Take pyridine, C₅H₅N. Nominal mass:
Odd nominal mass, one nitrogen (odd count) — consistent. Now take pyrimidine, C₄H₄N₂:
Even nominal mass, two nitrogens (even count) — also consistent: even N-count pairs with even mass, odd N-count pairs with odd mass.
Step 4 — extend to fragmentation parity. Because M⁺• has an odd number of electrons (a radical cation), simple homolytic bond cleavage that ejects a radical neutral fragment leaves an even-electron cation behind — and that cation's nominal mass necessarily differs from M by an odd number if the lost neutral radical contains an odd number of H atoms relative to its heavy-atom parity (most simple alkyl radical losses, e.g., loss of •CH₃, 15 Da, or •C₂H₅, 29 Da, are odd-mass losses from an odd-electron ion, producing an even-electron fragment ion at a mass that is even relative to M if M was odd, or odd if M was even — in short, simple single-bond homolysis flips the odd/even mass parity between M⁺• and the resulting fragment cation). Rearrangement fragmentations (e.g., McLafferty rearrangement, loss of a stable even-electron neutral like an alkene) instead preserve the parity, because two bonds change in a concerted process and the neutral lost is even-electron, leaving the fragment ion odd-electron and of even-mass-loss relative to M. This parity bookkeeping — nitrogen rule for the intact molecule, parity-flip-vs-parity-preservation for fragment identification — is exactly the toolkit used to distinguish simple cleavages from rearrangements in real spectra, and it only works because the starting molecular ion's electron count and mass parity are fixed unambiguously by the EI mechanism itself.
Worked examples
Example 1 — Foundational: locating M⁺• and checking the nitrogen rule for a simple ketone. 2-Hexanone, CH₃COCH₂CH₂CH₂CH₃ (C₆H₁₂O), is ionized by EI. Predict the m/z of M⁺• and confirm the nitrogen rule. Molecular formula: C₆H₁₂O. Nominal mass using ¹²C = 12.000, ¹H = 1.008 (rounded to nearest integer for nominal mass, ¹H ≈ 1):
Zero nitrogen atoms (an even number, namely zero), so the nitrogen rule predicts an even nominal mass — and indeed is even. Consistent. The molecular ion appears at
carrying a single positive charge and one unpaired electron, formally written [C₆H₁₂O]⁺•. In the real EI spectrum of 2-hexanone, M⁺• at m/z 100 is observed but weak (typically only a few percent relative intensity), because aliphatic ketones fragment efficiently by α-cleavage adjacent to the carbonyl. The dominant fragment, loss of •C₄H₉ (57 Da) from the alkyl side, gives the acylium ion at
corresponding to CH₃C≡O⁺, which is the base peak. Note the mass parity flip predicted above: M⁺• (even mass, 100, odd-electron) loses an odd-mass radical (•C₄H₉, 57) to give an even-electron fragment cation at odd mass (43) — exactly the homolytic-cleavage parity rule from the second derivation.
Example 2 — Applied: distinguishing M⁺• from a contaminant/background peak in a GC-MS trace, using appearance-energy logic and neutral-loss plausibility. A GC-MS analysis of an unknown eluent shows a peak cluster with the highest-mass ion at m/z 150, next most prominent ions at m/z 135, 122, and 107, with 150 present at only 2% relative intensity. A colleague suggests the true molecular ion might instead be an unnoticed shoulder at m/z 164. Decide which assignment is chemically defensible. Check the neutral losses from the candidate M⁺• at m/z 150:
Every one of these losses corresponds to a chemically reasonable radical or small stable neutral — none fall in the notorious "forbidden gap" of 4–14 or 21–25 mass units below M (losses in those ranges essentially never correspond to simple bond cleavages or common rearrangements — there is no combination of H, C, N, O that plausibly loses, say, 5 or 22 mass units as a single stable fragment). This strongly supports m/z 150 as a legitimate, structurally consistent M⁺•. Now test the m/z 164 shoulder as an alternative M⁺•. The gap from 164 down to the next real fragment, 150, would be
a loss of 14 mass units — squarely inside the forbidden zone (14 Da would require loss of a bare CH₂ or N atom as a neutral, neither of which is a stable, chemically reasonable species to expel as a discrete fragment in a single step). Because a genuine M⁺• should never show a first fragmentation loss of exactly 14 Da, the shoulder at 164 is almost certainly a co-eluting background ion (a common column-bleed siloxane fragment or an unrelated trace contaminant) rather than the true molecular ion, and m/z 150 is the correct M⁺• despite its low relative abundance. This illustrates the general diagnostic principle: identifying M⁺• is not simply "find the highest mass peak" — it requires checking that every neutral loss down to the next real fragment is chemically plausible.
Example 3 — Exam/competition level: quantitative appearance-energy analysis to extract a bond dissociation energy inside the ion. The ionization energy of toluene (C₇H₈, M_r = 92) is measured as IE(toluene) = 8.83 eV. The appearance energy for the benzyl cation C₇H₇⁺ (m/z 91, formed by loss of a hydrogen atom, •H, 1 Da) from toluene's molecular ion is measured as AE(C₇H₇⁺) = 9.85 eV. Assume negligible kinetic energy release (a good approximation for this well-studied simple C–H cleavage). Estimate the effective activation energy for C–H bond cleavage within the toluene molecular ion, and compare it with the known gas-phase homolytic C–H bond dissociation energy of toluene's benzylic C–H bond, D(C₆H₅CH₂–H) ≈ 3.75 eV (≈ 90 kcal/mol). Using the appearance-energy relationship (with negligible translational energy release, so the excess-kinetic-energy term is dropped):
Solve for the activation energy:
This value, 1.02 eV (≈ 23.5 kcal/mol), is the energy required to break the benzylic C–H bond starting from the radical cation, not from the neutral. It is markedly smaller than the neutral-molecule bond dissociation energy of 3.75 eV, because removing an electron from the aromatic π-system of toluene dramatically weakens the adjacent benzylic C–H bond — ionization does not merely add a spectator charge, it fundamentally alters the electronic structure and bonding of the molecule. As a limiting-case sanity check: if ionization left the bonding entirely undisturbed (a naive "just remove an electron, change nothing else" model), one would expect , i.e., the cleavage energy inside the ion should equal the neutral bond dissociation energy of 3.75 eV. The measured value (1.02 eV) is far below this naive limit, which is the expected and physically required behavior — it confirms that the positive charge and unpaired electron in the toluene radical cation are strongly delocalized into the ring system, weakening exactly the bond whose cleavage generates the resonance-stabilized (tropylium/benzyl) cation. This is a general feature of EI fragmentation: cleavages that lead to resonance-stabilized product ions have anomalously low activation energies relative to the corresponding neutral bond strengths, precisely because the departing charge stabilizes the transition state.
Limiting cases, scope & common traps
| Situation | Expected behavior | Why |
|---|---|---|
| Electron energy at or just above IE (threshold EI) | Weak, energy-sensitive ionization; less fragmentation | Cross-section rising steeply near threshold; used in specialized "low-voltage EI" for enhanced M⁺• survival |
| Electron energy = 70 eV (standard) | Reproducible fragmentation pattern, library-matchable | Plateau region of σ(E); internal energy distribution stabilized |
| Highly branched alcohols, amines, some esters | M⁺• weak or entirely absent | Facile α-cleavage / dehydration channels outcompete survival to detector; low IE lowers barrier further |
| Aromatic and polycyclic compounds | Strong, often base-peak M⁺• | Delocalization stabilizes the radical cation; high barriers to fragmentation |
| Compound with odd number of N atoms | Odd nominal mass for M⁺• | Nitrogen rule (parity argument above) |
| Fragment ion from simple homolysis | Even-electron cation, odd-mass loss from M (typically) | Radical neutral departs, parity flips |
| Fragment ion from rearrangement (e.g., McLafferty) | Odd-electron cation, even-mass loss from M (typically) | Even-electron neutral departs, parity preserved |
| Apparent "M⁺•" with a 14 or 4–14 Da gap to next peak | Almost certainly not the true M⁺•, likely background/contaminant | No chemically reasonable single-step neutral loss in that mass range |
The chemist behind it
Electron ionization as a practical analytical tool owes its modern form largely to Arthur Jeffrey Dempster and, more directly for the organic-chemistry application, to the instrument-building tradition of Alfred O. C. Nier and the mass spectrometrists of the 1940s–50s petroleum industry, who needed to identify hydrocarbon mixtures from cracked crude oil. But if a single physicist's name is most tightly bound to the electron bombardment method itself, it is Dempster, who in 1918 built the first mass spectrometer to use electron impact for ionizing gaseous samples — displacing earlier positive-ray (canal-ray discharge) methods that were far less controllable and gave poorer mass resolution. Dempster's key insight was mundane-sounding but transformative: rather than relying on an uncontrolled gas discharge to generate ions of unknown and highly variable internal energy, use a well-defined, adjustable electron beam from a heated filament, accelerated through a known potential. This single change — controlling the ionizing agent's energy directly, rather than letting a plasma do it — is what eventually allowed later workers to standardize on a fixed 70 V acceleration and thereby build reproducible, library-comparable spectra. Dempster's 1918 instrument achieved roughly 1-in-100 mass resolution, primitive by modern standards, but the ionization method, not the mass analyzer, is what survives essentially unchanged in every EI source built since.
Origins · 1 minArthur Jeffrey Dempster and how this was discovered
Canadian-American physicist who designed the first electron-impact mass spectrometer (1918) and later discovered the fissile isotope uranium-235 (1935) by mass-spectrometric analysis of uranium's isotopic composition — a discovery that fed directly into the physics underlying the atomic bomb program. His electron-bombardment ion source design, refined through the following decades by Nier and others, remains the direct conceptual ancestor of every EI source in use today.
Why does EI need such high vacuum, and what happens if the vacuum is poor?
EI sources typically operate at 10⁻⁵–10⁻⁶ torr so that the mean free path of ions and electrons is long compared to the source dimensions — ions must reach the exit slit without colliding with residual gas molecules, which would scatter them, cause unwanted ion-molecule reactions, or quench the carefully controlled internal energy distribution that gives EI its reproducibility. Poor vacuum introduces background peaks (commonly water at m/z 18, nitrogen at 28, and column-bleed siloxanes around m/z 207, 281, 355), broadens or shifts peak shapes, and can produce spurious "chemical ionization-like" adduct peaks from ion-molecule collisions that were never intended. Because EI's entire analytical value rests on physics happening to isolated, collision-free molecules and ions, vacuum integrity is not a peripheral detail — it is foundational to the method's reproducibility.
Why is the molecular ion sometimes completely absent from an EI spectrum, even for a stable, well-characterized compound?
Absence of M⁺• means every ionized molecule fragmented before reaching the detector — a kinetic competition, not a thermodynamic impossibility. If the activation energy for some fragmentation pathway (often a favorable rearrangement, like dehydration in alcohols or α-cleavage in amines) is small compared to the excess internal energy typically deposited at 70 eV, essentially all M⁺• decompose within the source's microsecond timescale. Lowering the electron energy toward threshold (low-energy EI, 10–20 eV) reduces the internal energy deposited and often recovers a visible M⁺•, at the cost of reduced total ion yield and loss of standard-library comparability. Chemical ionization is the more common practical remedy when molecular weight confirmation is essential and low-energy EI proves insufficient.
How is the nitrogen rule used in practice when interpreting an unknown spectrum?
After tentatively identifying a candidate M⁺• peak, check its nominal mass parity: an odd nominal mass implies an odd number of nitrogen atoms (1, 3, 5, ...), while an even nominal mass implies zero or an even number of nitrogens (0, 2, 4, ...), assuming the molecule contains only C, H, N, O, S, and halogens — the overwhelming majority of organic analytes. This is a fast, powerful triage tool: an unknown with M⁺• at m/z 121 cannot contain zero or two nitrogens: it must have one (or three, though three nitrogens at such low mass is chemically improbable), immediately narrowing candidate structures before any fragment-by-fragment analysis begins.
Does the nitrogen rule ever fail?
Yes — it assumes standard valences for all atoms present and that the ion is singly charged. It can fail for compounds containing elements with unusual valence behavior in the given structure, for multiply charged ions (rare but possible for large, easily multiply-ionized systems), or when non-standard isotopes dominate a sample (isotope-labeled internal standards, for example, deliberately shift nominal masses). It is best used as a strong presumptive check, always followed by confirming exact mass (via high-resolution MS) or consistent fragment-ion parities before finalizing a structural assignment.
Why is the molecular ion's exact mass, not just its nominal mass, valuable — and how does EI relate to high-resolution mass spectrometry?
Nominal (integer) mass from a low-resolution EI-quadrupole instrument cannot distinguish, for example, C₃H₄O₂ (nominal mass 72.000) from C₄H₈O (nominal mass 72.000) — same integer, different exact mass (72.0211 Da vs. 72.0575 Da) and different formula. High-resolution EI, run on magnetic-sector, Orbitrap, or high-resolution TOF instruments, resolves this by measuring m/z to four or five decimal places, allowing the exact elemental formula of M⁺• (and its fragments) to be assigned unambiguously. EI is entirely compatible with high-resolution analyzers — the ionization mechanism and the mass analyzer are independent choices — which is why "EI-HRMS" is a standard combination in rigorous structure elucidation work.
How does EI differ fundamentally from chemical ionization (CI) in terms of the ion formed?
EI directly ionizes the analyte molecule by electron impact, producing an odd-electron radical cation M⁺• with excess internal energy that often drives extensive fragmentation. CI instead ionizes a reagent gas (methane, isobutane, ammonia) first, then lets reagent ions transfer a proton (or hydride, or form an adduct) to the analyte in gentler, exothermic ion-molecule reactions, producing predominantly even-electron species like [M+H]⁺ with much less internal energy and therefore far less fragmentation. The two techniques are complementary: EI for rich structural fragmentation and library matching, CI for reliable molecular weight confirmation when M⁺• is weak or absent in the EI spectrum.
Why do aromatic compounds tend to show strong molecular ions while highly branched aliphatic compounds often do not?
Aromatic π-systems delocalize both the positive charge and the unpaired electron of M⁺• over several atoms, which lowers the energy of the radical cation relative to any transition state for fragmentation — in effect, raising the activation energy for bond cleavage relative to the (already lower) energy of the stable, delocalized ion itself. Highly branched aliphatic molecules, by contrast, have no such delocalization; instead, branching creates easily accessible low-barrier fragmentation pathways (tertiary carbocation-like fragment stabilization, facile α-cleavages at branch points), so M⁺• decomposes rapidly. This is a direct, general consequence of the competition between ion stability and fragmentation kinetics developed throughout this treatment.