Modeling Concepts - Potential Energy Surface
The above reaction profile is an example of a potential energy surface. A PES depicts the relationship between energy and geometry where geometry means the relative positions of atoms. Each point on the surface corresponds to a fully specified arrangement of atoms and the corresponding energy. The Y-axis is quite simple but the X-axis is masking some information. The X-axis may only indicate a single geomtry variable, but all other geometry variables are implied. This includes bond dissociation and formation, angle rotations, everything that changes in the reaction.
The rotation about the center bond of butane as a function of energy is another example PES.
In this example, there is a single geometry variable, the CCCC dihedral angle. As one rotates around the central C-C bond in butane, other bond lengths and angles adjust to compensate for steric clashes. These other geometry variables are not explicitly depicted in the graph. Adding them to the graph would add complexity and would probably not add much insight to the energetics of this system.
A Ramachandran plot is a classic PES of peptide conformational space. In that case, two dihedral angles are plotted and are therefore both the X and Y axes. The energy data is in the contour.
When you do a reaction in the lab or take a spectrum, you are working on an ensemble of molecules with a Boltzmann distribution of conformational states. When you do a calculation, you are usually modeling a single molecule! Thus you need to be aware of the conformational flexibility of your molecule and use the molecular modeling tools to explore its potential energy surface.
Exercise 3: Sketch a PES for an Sn2 reaction (perhaps Br- + CH3Cl). What are the major geometry variables that change throughout this reaction? You can google "sn2 PES" for some examples to check your own result. If it is awkward to sketch, it is fine to use one of these online images in your answer but please add some comments about the major changes that accur, not just in bond lengths, but also in bond angles.
You can go back to the main prelab page or go onto the next concept.