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Amino Acids
The Featured Molecules this month are the 20 standard α-amino acids found in proteins and serve as background to the paper by Barone and Schmidt on the “Nonfood Applications of Proteinaceous Renewable Materials”. The molecules are presented in two formats, the neutral form and the ionized form found in solution at physiologic pH. All structures have been minimized by a combination of the Amber force field and the 6-31G* basis set.
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. Viewing Requirements
In addition to the static images, two fully manipulable versions
(Jmol, MDLChime)
of these molecules appear below.
 Download
Chime (registration required)
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