We will determine the potential energy of butane as a function of rotation about the central dihedral angle. To do this, we will use the program Cerius2, which calculates the electronic structure and energies of molecules. In particular, we will use the semi-empirical method, AM1, to quickly calculate the electronic structure of butane. AM1 is found in the MOPAC suite of programs.
Do the following steps:
Build the Molecule
Choose "Build" in the upper menu bar, and then "3-D Sketcher".
In the 3-D Sketcher palette,
Mouse Button Review - Practice manipulating the molecule in the model window:
The left mouse button is the "normal" mouse button, used for selecting, etc.
The middle mouse button is for translating a molecule.
Middle and right buttons together zoom and shrink the molecule.
The right mouse button is for rotating molecules:
Moving the mouse up & down in the center of screen rotates about a horizontal line
Moving the mouse side-to-side in the center of screen rotates about a vertical line
Moving the mouse up & down at the side of the screen rotates within the plane of the screen
Obtain a Stable Starting Structure via Geometry Optimization using Semi-empirical Calculations
Click on the Menu Deck Bar (which by default is set at "Builders 1"), and choose "Quantum 1"
Within the Quantum 1 set of cards, choose "MOPAC". The MOPAC card will come forward.
Choose "Run". The card that appears is your interface for setting up a calculation the determine the electronic structure of your molecule.
In the Run dialog box, set the Task to "Geometry Optimization" and the Method to "AM1". Click on "RUN".
Check the resulting dihedral angle by selecting "Geometry" at the very top menu bar of cerius2, and then "Measurement" and choose the icon for a dihedral angle. Choose the four carbons sequentially to let the computer know which dihedral angle to measure.
Scan the Potential Energy Surface
To find the electronic potential energy as a function of dihedral angle, we need to tell the computer which dihedral angle to rotate about. To do this, on the MOPAC Deck (not at top menu bar) choose "Geometry" and then "Z-Matrix". Verify that the dihedral angle is line no. 9 (i.e., all four carbons listed on the line). Your instructor will help you with this.
On the RUN card, choose "Scan Potential Surface" as the task, and then select "More" next to the task. Fill in the Z-Matrix Line No. (i.e., put 9), select "Torsion", and have the torsion (i.e., dihedral) angle vary from 0° to 360°. Do about 50 steps within that range. Once these are all specified, click the "RUN" button on the "RUN" card.
Drag the mouse back and forth on the resulting potential energy graph to see the underlying structures.
Questions
Is the potential energy surface what you expected, based on your knowledge from previous classes?