This graph shows the potential energy for a N-C-O bond angle using a harmonic potential with the parameters given in the AMBER potential energy function. Such a term would partly control the angular vibrations of the carbonyl oxygen on the main chain of a polypeptide chain. The bond angle constant is 80 kcal/(mol.degrees^2) and the equilibrium bond angle () is 122.9 degrees. The dashed line indicates an energy of 0.29 kcal/mol which is equal to 1/2RT at a temperature of 300K. This is the energy that an individual degree of freedom can expect at this temperature and indicates that a this bond could be expect to be undergoing vibrations of the order of 4 degrees at room temperature. If we assumes that the N and C atoms remain mostly static then this would entail motion in this degree of freedom of the order of 0.09 Å for the oxygen atom (as the C-O bond is 1.229 Å long). It is interesting to compare this to a motion of approximately 0.03 Å amplitude to vibrations of the C=O bond (link to graph of this motion). (This is not quite the whole story as there would be another bond angle term for the atoms C_alpha-C-O also restricting the motion).

Oliver Smart

© O.S. Smart 1995, all rights reserved 

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