Modeling Concepts - Geometry - Coordinate Scan:

A coordinate scan is another way of searching the potential energy surface. In an earlier part of this prelab, we considered rotation about the CCCC dihedral angle of n-butane.

Butane: Energy vs Dihedral Angle - Potential Energy Surface
In a coordinate scan of this type, the dihedral angle is defined along with an increment, perhaps 10 degrees. The dihedral angle is varied from 0 through 360 degrees, with a stop at each increment (0, 10, 20 ......). At each increment step, all other bond lengths and angles are allowed to minimize but the dihedral angle is held fixed at the defined step. The energy of that geometry is calculated as part of the process. In the graph above, each circle was a geometry tested in this scan.

We also saw a Ramachandran plot, and these are also typically generated using a dual variable coordinate scan of the peptide phi and psi dihedral angles.

One can also follow bond breaking and bond making using a coordinate scan. In that case, one would vary a bond length.

Exercise 7: In an earlier exercise you sketched an Sn2 reaction profile. If you were to try to generate this profile using a coordinate scan, what variable(s) would you scan?

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