Chapter 12: Structure Determination: Mass Spectrometry and Infrared Spectroscopy
Electron-impact ionization produces the molecular ion M⁺
Mass spectrometry answers the most basic structural question about an unknown compound: its molecular mass. The instrument operates on ions rather than neutral molecules, so the first step is ionization. In the electron-impact technique, the vaporized sample passes through a beam of electrons accelerated to about 70 electron volts. A collision transfers enough energy to eject one electron from a molecule, generating a species that is simultaneously a cation and a radical — the molecular ion, written M⁺. Propane, for example, gives a molecular ion of m/z 44, the sum of three carbons (36) and…
Fragmentation favors the most stable carbocation
Electron-impact ionization deposits roughly ten times more energy in a molecule than any of its bonds requires, so most molecular ions decompose before detection. Each fragmentation splits the radical cation into two pieces: a cation, which the instrument records, and a neutral radical or molecule, which it does not. The resulting fragmentation pattern is a fingerprint of the carbon skeleton, and its logic is the chemistry of carbocations. A carbon–carbon bond cleaves preferentially when the positive charge can rest on the more substituted carbon, following the stability order tertiary >…
Isotope peaks and the nitrogen rule narrow the molecular formula
A molecular mass alone is compatible with many molecular formulas, but the fine structure around the molecular ion excludes most of them. Because most elements occur naturally as isotope mixtures, the molecular ion is accompanied by satellite peaks at higher mass, and the pattern of those satellites identifies specific elements. Carbon itself produces the most universal satellite. About 1.1% of carbon atoms are ¹³C, so every organic compound shows an M+1 peak whose intensity is roughly 1.1% of the molecular ion per carbon atom; a ten-carbon compound has an M+1 peak about 11% as tall as M⁺,…
Bond stiffness and atomic mass set vibrational frequencies
The electromagnetic spectrum spans radio waves to X-rays, and each spectroscopic method uses the portion whose photon energy matches a particular molecular process. Infrared photons carry the energy of bond vibrations. The atoms in a molecule are never at rest; each bond stretches and bends at definite frequencies, and when infrared light of a matching frequency strikes the molecule, the vibration absorbs that energy and the absorbed frequencies are removed from the transmitted beam. The record of missing frequencies is the infrared spectrum, plotted as percent transmittance against…
Four regions of the IR spectrum locate the functional groups
The practical power of infrared spectroscopy is that functional groups absorb at nearly the same frequencies whatever molecule contains them. A carbonyl stretch falls near 1715 cm⁻¹ in cyclohexanone, in butan-2-one, and in a fifty-carbon natural product alike. The spectrum is therefore read against a four-region map rather than band by band. The region from 4000 to 2500 cm⁻¹ contains the stretches of bonds to hydrogen. Band shape matters as much as position here. The O–H stretch of an alcohol, broadened by hydrogen bonding, is a wide, rounded absorption centered near 3350 cm⁻¹; carboxylic…
Mass spectrometry gives the mass; infrared names the groups
Faced with an unknown compound, a chemist applies the two techniques of this chapter in a fixed order, because each narrows the field the other must search. The mass spectrum is consulted first for three facts. The molecular ion's m/z fixes the molecular mass, and with it the short list of molecular formulas of that nominal mass. The parity of the mass invokes the nitrogen rule: an odd mass requires an odd number of nitrogen atoms. The isotope envelope is scanned for the halogen signatures — a 1:1 doublet for bromine, a 3:1 pair for chlorine — and the M+1 intensity offers a rough carbon…
Part of Organic Chemistry, a free and open textbook licensed CC BY-SA 4.0.