Mass spectrometry

Result

Mass spectrometry

T-081Home CU-302Threads quantum · structure

Statement

Molecular mass and structure from fragmentation.

Why it matters

The other results in this unit — rotational-spectroscopy, vibrational-ir-spectroscopy, uv-vis-electronic, nmr-chemical-shift — each probe how a molecule interacts with light of a particular energy. Mass spectrometry works completely differently: it ionises the sample and separates the resulting ions purely by mass-to-charge ratio, giving molecular weight directly and, through characteristic fragmentation, a map of the molecule's substructure. Combined with nmr-chemical-shift's environment-by-environment fingerprint and vibrational-ir-spectroscopy's functional-group signatures, it is one of the standard tools for solving an unknown structure from spectra, the synthesis lecture that closes this unit.

Hypotheses

The sample can be ionised, either with substantial, reproducible fragmentation (electron ionisation) or largely intact (soft ionisation methods).Different ionisation methods trade off informative fragmentation against preserving the parent molecular ion; the choice depends on the size and fragility of the analyte, and both approaches are used routinely for different classes of molecule. Ions travel through a high vacuum, so their trajectories are governed only by charge and mass, not by collisions with other molecules.Without a sufficiently high vacuum, collisions would scatter ions before they reach the detector, destroying the clean mass-to-charge separation the instrument depends on. For singly charged ions from electron ionisation, the observed \(m/z\) of the molecular ion equals the molecular mass directly.Soft ionisation methods (electrospray ionisation, matrix-assisted laser desorption/ionisation) commonly generate multiply charged ions, especially for large biomolecules, so the true molecular mass must be deconvoluted from a series of peaks at different charge states rather than read off a single \(m/z\) value.

Proof

\text{M} + e^- \rightarrow \text{M}^{+\bullet} + 2e^-

In electron ionisation, an energetic electron beam knocks an electron from the neutral molecule, forming a radical cation (the molecular ion) plus an ejected electron. A

\text{M}^{+\bullet} \rightarrow \text{fragment}^+ + \text{neutral loss}

The molecular ion typically carries substantial excess internal energy from ionisation and fragments at its structurally weakest or most stabilised sites, producing a reproducible, characteristic set of smaller cations and neutral losses. A

r \propto \sqrt{m/z}\ \ (\text{magnetic sector}); \qquad t \propto \sqrt{m/z}\ \ (\text{time-of-flight})

Ions are accelerated by a known electric field and then separated by mass-to-charge ratio — by radius of curvature in a magnetic field, or by flight time to a detector for ions given identical kinetic energy — lighter ions (at fixed charge) are deflected more, or arrive sooner, than heavier ones. A

\text{Spectrum: ion abundance vs } m/z

The detector records abundance as a function of \(m/z\); the molecular ion peak (when present) gives the molecular mass directly, and the pattern of fragment peaks — and, specifically, the mass differences (losses) between peaks — is diagnostic of substructure. A

\text{M:M+2 ratio} \approx 3:1\ (\text{one Cl}), \ \approx 1:1\ (\text{one Br})

Natural isotopic abundance of heteroatoms such as chlorine or bromine produces a characteristic, diagnostic ratio between the molecular ion peak and the peak two mass units higher, confirming the presence and number of such atoms independent of any fragmentation reasoning. A

Result

m/z_{\text{molecular ion}} \approx M_r, \qquad \text{fragment mass losses reveal substructure}

Reading. Mass spectrometry reports the mass-to-charge ratio of the intact ionised molecule (usually its molecular weight, for a singly charged ion) together with a pattern of characteristic mass losses that reveals structural fragments.

Scope. Requires the analyte be ionisable, and reasonably volatile and thermally stable for classical electron-ionisation instruments, or amenable to a soft-ionisation method for larger or more labile biomolecules; fragmentation patterns are empirically characteristic and interpreted by comparison with known behaviour, not derived from first principles alone.

Corollaries & converses

Combined with nmr-chemical-shift's per-environment fingerprint and vibrational-ir-spectroscopy's functional-group signatures, mass spectrometry's molecular-weight and fragmentation data narrows candidate structures for an unknown compound far faster than any single technique alone.
High-resolution mass spectrometry, measuring \(m/z\) to several decimal places, distinguishes candidate molecular formulas sharing the same nominal (integer) mass — e.g. CO and N\(_2\), both nominal mass \(28\), differ measurably at high precision because carbon, nitrogen, and oxygen's exact atomic masses differ.
Converse: given a known compound's structure, its expected fragmentation pattern and molecular ion mass can be predicted in advance, and used to confirm the identity or purity of a synthesised product.

Fails without

Apply classical electron-ionisation MS directly to a large, thermally fragile biomolecule (violating the ionisability/stability hypothesis): the sample decomposes or fragments too extensively before or during ionisation to yield an interpretable molecular ion at all; a soft-ionisation method must be used instead.
Read \(m/z\) as mass directly for an ion produced by a soft-ionisation method without checking its charge state (Hypotheses' t3 caveat): a multiply charged ion's \(m/z\) is only a fraction of its true mass, and dividing by the wrong assumed charge gives a badly incorrect molecular mass.

Common errors

Assuming the highest-\(m/z\) peak observed is always the molecular ion; it can be entirely absent if fragmentation is extensive, or a small isotope or adduct peak can appear at even higher mass.
Confusing nominal (integer) mass with exact mass, and missing that high-resolution instruments can distinguish formulas of equal nominal mass.
Assuming fragmentation always breaks the structurally "weakest-looking" bond on paper, rather than reflecting the relative stability of the resulting fragment ions (e.g. carbocation stability).
Misreading a diagnostic M+2 isotope peak (from Cl, Br, or S) as evidence of sample impurity rather than as expected natural-abundance isotope signal.

Discussion

Mass spectrometry traces to J.J. Thomson's early-20th-century work on positive rays, which also led to the discovery of isotopes, and was refined into a precision analytical instrument by Francis Aston's mass spectrograph shortly afterward. The technique has since become one of the standard tools across analytical, organic, and biological chemistry, including large-scale protein identification (proteomics).

Soft ionisation methods developed later — electrospray ionisation and matrix-assisted laser desorption/ionisation — allow large, fragile biomolecules such as proteins to be ionised largely intact rather than extensively fragmented, but commonly generate multiply charged ions. Determining the true molecular mass from such data requires deconvoluting a series of peaks at different charge states rather than reading a single \(m/z\) value directly, a genuinely different data-analysis problem from classical electron-ionisation spectra.

Common misconception: that mass spectrometry is a form of light-absorption spectroscopy, like IR or UV-visible. It is not: no photon absorption or emission is involved at any stage, only ionisation and mass-based separation — it is grouped with the spectroscopic techniques here purely because it is part of the same structure-elucidation toolkit, not because it shares their underlying physics.

Worked examples

\text{Ethanol}, M_r=46: \text{ molecular ion at } m/z=46, \text{ fragment at } m/z=31

The mass loss of \(46-31=15\) corresponds to loss of a methyl radical (\(\bullet\text{CH}_3\), mass \(15\)), consistent with cleavage adjacent to the hydroxyl-bearing carbon — a standard, diagnostic fragmentation for this substructure. A

\text{Chlorobenzene: } m/z=112\ (\text{M}),\ 114\ (\text{M+2}), \text{ ratio} \approx 3:1

The observed \(\approx3:1\) ratio between the molecular ion and the peak two mass units higher directly matches the natural \(^{35}\text{Cl}:^{37}\text{Cl}\) abundance ratio, confirming exactly one chlorine atom is present in the molecule. A

\text{Molecular ion} \Rightarrow \text{mass}; \quad \text{fragment losses} \Rightarrow \text{substructure}; \quad \text{isotope pattern} \Rightarrow \text{heteroatom content}

Reading. Three independent lines of evidence within a single spectrum — molecular ion mass, fragment mass losses, and isotope pattern — together narrow down a candidate structure substantially.

Scope. The same three-part reading strategy applies to any electron-ionisation mass spectrum of a small, volatile organic molecule.

Problems

A molecular ion at \(m/z=88\) shows a prominent fragment at \(m/z=73\). Identify the most likely neutral fragment lost.
Solution
Mass loss \(=88-73=15\), matching loss of a methyl radical (\(\bullet\text{CH}_3\)), the single most common small-mass loss seen adjacent to a branch point or heteroatom-bearing carbon.
Explain, qualitatively, why a dichlorinated compound shows an M:M+2:M+4 pattern in roughly a \(9:6:1\) ratio rather than the simple \(3:1\) M:M+2 ratio seen for a single chlorine.
Solution
With two chlorine atoms, each independently \(^{35}\text{Cl}\) or \(^{37}\text{Cl}\) with roughly \(3:1\) natural abundance, the possible combinations (both \(^{35}\text{Cl}\), one of each, both \(^{37}\text{Cl}\)) follow a binomial expansion of that \(3:1\) ratio, giving relative probabilities close to \(9:6:1\) for M, M+2, and M+4 respectively — the same isotope-pattern logic as the single-chlorine case, simply compounded over two independent atoms.
Explain how high-resolution mass spectrometry could distinguish CO (exact mass \(27.9949\)) from N\(_2\) (exact mass \(28.0061\)), even though both have nominal mass \(28\).
Solution
A high-resolution instrument measures \(m/z\) to several decimal places rather than to the nearest integer; since carbon, oxygen, and nitrogen's exact isotopic masses differ measurably from integer values in slightly different ways, CO and N\(_2\) — identical in nominal (integer) mass — are resolved as two distinct peaks at high enough mass resolution, whereas a low-resolution (unit-mass) instrument would report them as a single, indistinguishable peak at \(m/z=28\).