Experiment #11 - Conformational Isomerism in n-Butane

General Procedure: Use BUILD to construct molecule & apply dihedral angle constraints. Save the file. Use the SETUP menu to set up the AM1 calculation & submit the job. Use the DISPLAY menu to view the output.

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Set up different conformers using the BUILD menu. Enter the BUILD by choosing NEW from the FILE menu on the green Spartan screen. This brings up the black BUILD screen. With the left mouse button, click on the tetrahedral C & then click mouse at a position in the window. The first C with four H's will appear. Position cursor at end of a bond & click. Another C will be bonded to the first. H's will appear in correct number & in staggered position. Continue to finish butane with CCCC dihedral angle approximately = 180o. In the GEOMETRY menu, choose DIHEDRAL. Pick (click on each of) the 4 C's & the program will tell you exactly what the torsional angle is. Type the number that you want to set the dihedral to in the box. Constrain the angle to 180 by choosing CONSTRAIN DIHEDRAL from the GEOMETRY menu. Choose SAVE AS from the file menu & save as expt11/butane180. This puts the file butane180 in the directory expt11. Quit the BUILD screen by choosing FILE, then QUIT. This puts you back into the green Spartan screen where butane180 will be displayed. Remove the molecule from the screen by choosing FILE, then CLOSE.

Use this same procedure to get the other conformers. From the FILE menu, choose NEW & build another butane, following the procedure above. This time, set the dihedral to 150 & constraint it to 150. SAVE AS butane150. Repeat for the other conformers.

To calculate the energy of each conformer, select a conformer by choosing FILE, then OPEN from the menu on the green screen. Spartan will display your directories and you can choose (click on) which conformer you want to work with. Spartan will display this molecule on the green screen. Then, from the SETUP menu, choose SEMIEMPIRICAL. Be sure the settings are: AM1, GEOMETRY OPTIMIZATION, and CONSTRAINTS (The latter applies the constraints that you gave during BUILD). Give the calculation a meaningful TITLE. Click on SAVE. Then choose SUBMIT from the SETUP menu. The program will tell you that the job is running & will "beep" when it has completed. Go to the DISPLAY menu & choose OUTPUT. Scroll through the output to check: title, dihedral angle constraint, final heat of formation & final dihedral angle. Record. Repeat for other conformers.

MOLECULAR MECHANICS CALCULATIONS. Follow the same procedure as above for each of the files that have already been created using the SYBYL & MMFF94 force fields. Use the SETUP menu as before, except this time, choose MECHANICS. In this setup, give the calculation a new title, choose GEOMETRY OPTIMIZATION, CONSTRAINTS, & SYBYL (or MMFF94). SUBMIT the job. A message will appear that the wavefunction & properties will be regenerated. Click OK. When the job has finished, DISPLAY the OUTPUT. Record the values.

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RELATIVE ENERGY: Calculate the relative energies of the conformers for the AM1 computational technique. Find out which conformer has the lowest absolute value of the energy. Set that value to zero & calculate the energy of all other conformers relative to that. For example: conf1 (10 kcal/mol), conf2 (-15 kcal/mol), conf 3 (0 kcal/mol). Conf2 has the lowest energy, conf1 is 25 kcal/mol & conf3 is 15 kcal/mol higher in energy, respectively).

Repeat the calculation of the relative energies of the conformers using the SYBYL & then MMFF94 results. Plot each on the same graph—one curve for AM1, one curve for SYBYL, & one curve for MMFF94. The relative energy is the Y-axis; the torsional angle (0 – 180) is the X-axis.

Do the three different methods predict the minimum and maximum energies to occur at the same torsional angles? How do we know these techniques give the correct answer?