The amino acids offer students a rich range of structural features to observe and to attempt to rationalize using simple bonding models. For example, students could be asked to suggest reasons for the difference in geometry around the two nitrogen atoms in the neutral form of glutamine, or to compare bond lengths and bond angles between a neutral amino acid and its ionized form.

Most computed structures are for single molecules in vacuo. Included in this month’s collection are models for both neutral alanine and its zwitterion that represent the average of ten structural calculations of each molecule in a periodic box of 216 water molecules. Students might wish to measure various structural parameters to see if the solution structures differ significantly from the structures in vacuo.

Also included this month is a brief video of a molecular dynamics simulation on neutral alanine representing approximately one picosecond at 555 K. This video could serve as an introduction for beginning students to the phenomena of internal molecular motion.

Lastly, students could verify that, with the exception of cysteine, the chiral carbon atoms are of S symmetry. In cysteine, the presence of the sulfur alters the order of precedence in the R/S system, and the chiral carbon is R. In all of these cases, the amino acids are structurally related to L-glyceraldehyde, and are referred to as L-amino acids.

Fully manipulable (Chime and Jmol) versions of these and other molecules are available at the JCE Digital Library Web site.