Mass Spectrometry & Infrared Spectroscopy: Alkyl & Carbonyl Groups

Instructor: Justin Wiens

Justin teaches college chemistry and has Bachelor and Doctorate degrees in chemistry.

In this lesson, we discuss how mass spectrometry and infrared spectroscopy can be used to probe the structure of molecules containing alkyl and carbonyl groups.


Chemists can use the tools of mass spectrometry and infrared spectroscopy to solve the 'mystery' of a molecule's true structure, or determine the identity of an unknown molecule. Forensic investigators often rely on these and other chemical techniques to analyze evidence found at a crime scene. Each approach shows advantages and disadvantages. Mass spectrometry can identify the mass of a molecule by detecting any fragments formed when the molecule is ionized in a mass spectrometer. However, no direct information is given on the types of chemical bonds present in the molecule. On the other hand, infrared spectroscopy cannot measure the mass of a molecule, but it can determine the types of chemical bonds present. In infrared spectroscopy, chemical bonds between atoms are excited with light. As a result, the bonds vibrate and the two atoms' positions oscillate relative to one another. These two techniques together are a powerful tool in determining a molecule's identity.

Mass Spectrometry

In mass spectrometry, electrons are typically used to ionize neutral molecules (M) in the sample, and the ions formed will have a positive charge of at least +1, corresponding to loss of one electron. The mass spectrometer actually measures the mass-to-charge ratio, m/z, corresponding to the mass of the ion if only one electron is lost (M+), or half of its mass if two electrons are lost (M2+), and so on. Note that it is impossible to lose, say, half an electron, as the electron is the fundamental unit of negative charge. In the discussion here, we will focus on cases where all ions have a +1 charge (this is the most common situation in mass spectrometry).

The electrons often have enough energy to excite chemical bonds, too. The ionization process therefore often leads to fragmentation of the parent molecular ion, M+, into daughter ions, X+. The mass spectrum includes peaks from the X+ and M+ ions, with the relative amounts of each daughter or parent ion typically plotted as relative intensity, as shown in the mass spectra below. We can often solve the puzzle of an entire molecule's identity by putting the 'pieces'--the fragment ions--together. To solve the puzzle, we must realize that the largest peak in a mass spectrum usually corresponds to the most energetically stable ion. If an ion is not stable, we would not expect to see it hang around for us to measure! Sometimes the M+ peak is the dominant one in a mass spectrum, but not in every case. The X+ fragment ions are sometimes more stable than M+.


For a simple hydrocarbon, which is a molecule that has H atoms bonded to C atoms, we typically observe the M+ peak, in addition to M+ peaks corresponding to loss of additional -CH2 (methylene) or -CH3 (methyl) groups, depending on what part of the molecule fragments. Even larger fragments can break off, too. Thus, we would observe peaks at m/z = M, M-14 (loss of a CH2), M-28 (loss of CH3 CH2), and so on. When the hydrocarbon is branched, the alkyl substituents ('branches', e.g. with a mass of B) coming off the carbon backbone (the 'tree') are often most easily snapped off, giving rise to an ion at m/z = M-B. A sketch of the mass spectrum for 2-methylbutane is shown below to demonstrate this point. If you are interested, you can find the measured spectrum from a number of different resources, including the online NIST chemistry webbook. Note the strong peak at m/z = 43. What fragment ion is this?

2-methylbutane mass spectrum

Carbonyl-containing Molecules

The carbonyl group consists of a carbon atom doubly bonded to an oxygen atom and is written as C=O. Carbonyl groups are commonly encountered in chemistry and are quite stable. As a result, side chains attached to the carbonyl are typically broken off; it is much rarer for the C=O groups itself to fragment. Actually, the carbonyl group can change form in rearrangement processes, but we only focus on fragmentation processes here. One thing that makes an X+ion with a carbonyl group relatively stable is the fact that the oxygen atom has a lone pair that can participate in resonance:

Acylium Ion

The resonance stabilizes this ion, called an acylium ion. R can be H or an alkyl or aromatic group. Therefore, we would expect a strong peak at the mass of the acylium ion in the mass spectrum. An example is shown below for the molecule 2-hexanone. Note the strong peaks at m/z = 43 and 58.

2-hexanone mass spectrum

There may be many other peaks in the mass spectrum of a particular molecule, and it is often possible to consider a unique mass spectrum as a sort of 'fingerprint' for an unknown molecule's identity by comparison with a spectrum database of known molecules.

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