Setting up a Model System for Dihedral Angle Potential Energy Calculations
To test the energy barrier to rotation about a dihedral angle in a polymer one needs to create a model for the dihedral in question. We begin with polyethylene (PE) as our test case. Our model for the dihedral angle in PE is butane.
Create a butane molecule using the Builder.
Use the
Fragment /Get command and select Ethyl, then Execute. Click on one of the hydrogens of the ethyl group that appears on the screen. Then click on a second ethyl in the Fragment Library. The program will automatically link up these two molecule. They should be in a trans configuration corresponding to a dihedral angle of 180 degrees. Save this molecule as bu180.car using the Molecule/Put command.To alter the dihedral angle use the
Modify/Geometry command in the Builder submenu. Select Dihedral as the geometry type. Then input 175, click on the box labeled Atom 4 in the menu and then click successively on each of the four carbon atoms. Once you select Execute you should see the molecular geometry change. Once you have generated a new geometry you will need to this new structure. You could call it bu175.car.Continue using this procedure to create molecules with dihedral angles that range from 0 to 180 degrees in increments of 5 degrees.