Finding the structure of a new molecule, whether a small one synthesized in the laboratory or a large protein found in living organisms, is central to the progression of chemistry and biochemistry. The structure of an organic molecule is usually determined using spectroscopic methods, including mass spectrometry and infrared spectroscopy. Mass spectrometry (MS) tells the molecular weight and formula of a molecule; infrared (IR) spectroscopy identifies the functional groups present in the molecule.

In small-molecule mass spectrometry, molecules are first ionized by collision with a high- energy electron beam. The ions then fragment into smaller pieces, which are magnetically sorted according to their mass-to-charge ratio (m/z). The ionized sample molecule is called the molecular ion, M⁺, and measurement of its mass gives the molecular weight of the sample. Structural clues about unknown samples can be obtained by interpreting the fragmentation pattern of the molecular ion. Mass-spectral fragmentations are usually complex, however, and interpretation is often difficult. In biological mass spectrometry, molecules are protonated using either electrospray ionization (ESI) or matrix-assisted laser desorption ionization (MALDI), and the protonated molecules are separated by time-of-flight (TOF) mass analysis.

Infrared spectroscopy involves the interaction of a molecule with electromagnetic radiation. When an organic molecule is irradiated with infrared energy, certain frequencies are absorbed by the molecule. The frequencies absorbed correspond to the amounts of energy needed to increase the amplitude of specific molecular vibrations such as bond stretching and bending. Since every functional group has a characteristic combination of bonds, every functional group has a characteristic set of infrared absorptions. For example, the terminal alkyne ≡C–H bond absorbs IR radiation of 3300 cm^–1, and the alkene C═C bond absorbs in the range 1640 to 1680 cm^–1. By observing which frequencies of infrared radiation are absorbed by a molecule and which are not, it’s possible to determine the functional groups a molecule contains.