How to Determine the Structure of an Organic Compound

The main steps are as follows:

1. Determining the empirical and molecular formulas

• Percentage composition: the mass percentage of each element (carbon, hydrogen, oxygen, etc.) is measured by quantitative elemental analysis.
• Empirical formula: the simplest ratio between the atoms is calculated from the percentages.
• Molecular formula: the exact molecular weight is determined by mass spectrometry (MS) or classical methods, which allows us to go from the empirical formula to the real one (for example, to know whether a CH₂ unit is repeated 2, 4 or 6 times).

2. Calculating the index of hydrogen deficiency (IHD, or degree of unsaturation)

It gives the number of double bonds, triple bonds or rings (cycles) in the molecule. It is calculated from the molecular formula with the following relation for hydrocarbons and their derivatives:

where C, H and N are the numbers of carbon, hydrogen and nitrogen atoms.

3. Structure elucidation by spectroscopy and physical methods

To know exactly how the atoms are bonded and to distinguish between different isomers, instrumental techniques are used:

• Infrared spectroscopy (IR): identifies the functional groups present (such as hydroxyl –OH, carbonyl C=O, amine –NH₂ or alkene C=C groups) from the vibration frequencies of the bonds.
• ¹H and ¹³C nuclear magnetic resonance (NMR): the most powerful technique; it reveals the “skeleton” of the molecule, the number of equivalent hydrogens or carbons, their chemical environment and which ones are neighbours.
• Mass spectrometry (MS): besides giving the molecular weight, the fragments into which the molecule breaks provide clues about branching and substructures.
• X-ray diffraction: if the compound forms crystals, it gives the exact three-dimensional geometry and the position of every atom in space.

A complete course on how to determine organic structures is available to you.