We explored amino acid side chains from a quantum mechanical perspective in order to identify molecular similarities and differences, for the purpose of exploring the de novo design of peptidic sequences with desired biochemical reactivities. Charge densities for the 20 genetically encoded amino acids in both alpha and beta conformations were partitioned into molecular fragments, and their electronic properties (charge, energy, and dipole and quadrupole moments) were calculated using atoms in molecules theory. Transferability, as required by this theory, was confirmed for the side chains. Two methods were used to identify similarity: The first mapped each side chain property vector onto frequency differentiated Andrews plots, while the second used a composite measure of vectorial distance and angle as the dependent variable for hierarchical cluster analyses. We found that both methods clustered the side chains into chemically related groups only on the basis of theoretically derived variables. Both fine grained and coarse grained levels of analysis highlighted important emergent properties such as hydropathy, polarity, size, aromaticity, and the presence of carbon chains (aliphatics) and hydroxyl groups (alcohol). These results verify the hypothesis that symmetries of charge densities (as measured by the variables used here) can account for the observed chemical reactivities of amino acids.