where R is a group known as the side chain. (Does the structure of proline below seem consistent with this formulation?)
(You must have the CHIME plug-in installed in order for the embedded structures in this document be visible. If you do not have Chime, you can get it at the Chime home page. You have control over various aspects of how the molecule is displayed, the rendering style, rotation, color scheme etc. Details on using Chime can be found at Eric Martz's site at U. Mass. Amherst.)
In this structure there has been an intramolecular proton transfer from the OH of the carboxylic acid group to the amine group. The two structures of glycine are shown here:
In the structure below, the zwitterion form of glycine has been superimposed over the non-zwitterion form so that you can see the extent of structural change caused by the proton transfer (the two molecules were superimposed by making the C-N bonds coincident). This is a little tough to see (as the change is small). Try several views in Chime, and try it with labels on and off, to ensure that you see the difference. Don't forget that you can change the size of the molecule (within limits) by holding down the SHIFT key and dragging the mouse with the (left) button held down (this and other ways of changing the structure are described on the U. Mass. page linked at the top of this page).
If we calculate the atomic charges on all atoms in the two forms of glycine, we obtain the results below (non-zwitterion form first - calculations performed using the PM3 semi-emperical method).
Do the computed charges seem consistent with the atoms and species involved? (Note that the charges are based on the energy minimized structure, so the charges on the two O's in the zwitterion are different since the calculation does not take into account free rotation about the C-C bond which would render the O's equivalent.)
As an introduction to the basics of peptide structure, here are two structures of the zwitterion form of the dipeptide glygly (glycylglycine). Find the peptide linkage in each structure. Is the geometry about the peptide linkage what you expected? One of these structures has been geometry optimized to minimize non-bonded repulsions and one has not. Which is which? How did you reach this conclusion?
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