Determination of structures of small molecules: Mass spectrometry

The first segment of small molecular structure determination is mass spectrometry. Simply speaking, if you want to deduce what a molecule is, one way of doing this is to measure the mass of it.

Let's say someone identifies an unknown animal. You weigh it and it weighs 7000 kg. You know elephants weigh 7000 kg. The unknown animal may possibly be an elephant!  (Stupid analogy, but it's the idea that counts)

The first problem in this method is that molecules are very small. For example, if the mass of an atom was mass of a elephant. The mass of an actual elephant would be larger than the mass of the moon. Because we are dealing with such small masses, we use a different unit of mass when we are talking about molecules. The unit we use is called the Dalton or Da.

1 Da= 1.66 x 10 ^-27 kg

How do we measure such small masses? With a miraculous machine called the mass spectrometer.

The mass spectrometer
The original mass spectrometer was very simple. Take a compound and heat it up so it vaporises into a gas. With the molecules now in the gas phase, fire high speed electrons at them to knock out an electron from them. This leaves a positively charge ion (a cation of the molecule).

This cation can be accelerated using its charge (passed through a potential difference). The positively charge molecule is then pass through a magnetic field which deflects charged molecules.

The charged molecules hit a detector. How much the molecule has deflected is based on its mass. Lighter molecules (the blue line) get deflected more than heavier molecules (the red line). A chemist can judge the mass of a molecule based on where it hits the detector.

Mass spectrometry in action

Suppose a chemist synthesized a molecule called aniline. Aniline is a very important compound that is used to make many chemicals including pharmaceuticals.

To check whether it is indeed aniline that was synthesized, he runs it in a mass spectrometer and this is what the machine gives out.

Now, the chemist knows he has aniline and can continue his research to save the world.

What happens if two things have the same mass?

One could easily envisage a problem with the above scenario. What if the chemist didn't know what molecule he had? The mass spectrometer tells you that a molecule has a mass of 93 Daltons, but many molecules have that mass. 

It's like asking, "I know the person I am interested is 93 kg, which individual in the world is it?" There are many people in the world that weigh 93 kg, so mass spectrometry alone doesn't always provide the answer. This is where IR spectroscopy and NMR spectroscopy come to the rescue.