Mass Spec, IR and UV

Learn.

You have an unknown sample of a organic compound you made in the lab. It may be the next great drug to treat an elusive disease. But how do you go about determining what molecule you are dealing with?

Combustion analysis can be used to determine the empirical formula of an unknown hydrocarbon. This is done by burning a hydrocarbon to completion. The below equation represents the reaction that will take place.

Hydrocarbon + Oxygen –> Water + Carbon Dioxide

The precise amount of oxygen burnt is known. Additionally, the amount of water and carbon dioxide released after the reaction is known. Hence using the conservation of mass law in a chemical equation, the initial mass of the hydrogen, carbon and oxygen can be found by adding the weight of the carbon dioxide and water together and subtracting the mass of oxygen. The molar ratio of water to carbon dioxide can then be used to determine the ratio of carbon: hydrogen : oxygen in the sample and dividing by the smallest number will give you the empirical formula.

The empirical formula is the smallest integer ratio between the constituent atoms in a molecule. Whereas, the molecular formula is the ratio of atoms which are found in a molecule – not this smallest number ratio. For example glucose empirical formula is CH2O whereas its molecular formula is C6H12O6.

Ok, so now you know you molecules empirical formula, how do you determine its molecular formula.

Mass spectrometry can help with this. By bombarding your unknown molecule with a high power electron beam you can knock away electrons, creating a molecular ion. This is similar to blowing the seeds off a dandelion. You can now accelerate the charged ion in an electric field. The resulting moving charged particle enters a magnetic field resulting in it curving. The longer the ion takes to curve, the heavier it is, just as a motorbike could turn faster the a semi trailer. This allows the mass/charge ratio to be determined hence the identity of the molecule can be determined.

Features of mass spectrum include it’s molecular ion which is how you determine the mass of the ion hence the molecular formula. The base peak is the most frequently occurring ion and is set to 100% as a reference peak. The daughter ion’s are a result of the method used to ionize the sample and are just the molecule being split into smaller molecules (they can be used to determine functional groups – but this is time intensive).

Bromine and chlorine distribution characteristics can be used in a mass spectrum to determine the presence of Bromine and chlorine ions.

The formula for degree of unsaturation (or double bond equivalence or index of hydrogen deficiency):

This simply tells you how many double bonds are present in a molecule and adding one for every ring present.

Infrared spectroscopy (IR) works by the bonds between molecules absorbing light at certain wave lengths. Different bonds absorb light at different wavelengths hence analyzing the absorption spectrum can provide insights into what functional groups are present. The following are ways of molecules absorbing light.

This table can be used to determine what molecules are absorbing light.

UV-Vis spectroscopy works by and can be used on organic compounds to determine whether a molecule is conjugated. Conjugated molecules have alternating double and single bonds, light in the UV-Vis spectrum can be absorbed due to the nature of these bonds. Hence is an organic molecule has a UV-Vis reading it is usually an indication that it is conjugated.

Memorize.

Formula for degree of unsaturation

Master.

State whether the following are empirical or moleculer compounds.

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