Experiment #6 - Substituent and Solvent Effects on Tautomeric Equilibria

Construct 1a, 1b, & 1c with (R=H): From the FILE menu, choose NEW. This will put you into the BUILDER. To build 1a, choose the sp² N from the atom types on the right. Click at a position on the central screen. The N will appear. Rotate it using the mouse so that it is easy to add the other atoms. Add the sp² C by choosing it from the right & clicking at the end of the yellow bond line on the N. Repeat for the other C's.

To make the ring, choose BOND from the top menu & click on the two yellow bond lines from atoms with the same valence. As you construct the molecule, try to set it up as close as possible to the picture. You may need to rotate the atoms around a central bond in order to change the dihedral angle so that the atoms line up in a ring.

TO ROTATE ATOMS AROUND A CENTRAL BOND: Double click on the bond with the left mouse button. The solid bond line will become a dotted line. Hold down the space bar & middle mouse button. Use the cursor to rotate whatever part of the molecule you need to around the bond in order to get the orientation you need to continue adding more carbons to make the ring.

After constructing the molecule, choose MINIMIZE from the top menu to do a molecular mechanics minimization to get a good starting structure for the AM1 calculation. In the FILE menu, choose SAVE AS to save the molecule as 1a (or expt6/1a). Then QUIT the FILE menu & go to the SETUP menu. Choose SEMIEMPIRICAL. Give the calculation a title, such as: AM1 Geometry Optimization of 1a. Also choose AM1 & GEOMETRY OPTIMIZATION. SAVE. Again enter SETUP & choose SUBMIT. When the calculation is complete, look at your molecule on the screen. You can see that it's geometry has been optimized.

[If it looks weird (long bonds, strange geometry), then you probably forgot to minimize it with molecular mechanics to get a good starting structurefor the AM1 calculation. Go back to the BUILD menu. Choose EDIT STRUCTURE & MINIMIZE. Then SAVE AS using the same name as before will replace the old geometry with the minimized one. Go back to SETUP & resubmit the AM1 geometry optimization.]

After the AM1 geometry optimization is complete, enter the DISPLAY menu & choose OUTPUT. Record the final heat of formation. Under the FILE menu, choose CLOSE to clear the screen of 1a. Then, repeat for 1b & 1c with R=H. NOTE: 1b & 1c each contain one tetrahedral C (i.e. sp³ atom type), as opposed to 1a, which has none. So be sure to make the correct selection in the BUILD menu when constructing 1 & 1c.

To construct 1a-1c with R=Cl, edit the 1a-1c structures with R=H. For example, to build 1a with R=Cl, in the FILE menu choose OPEN. When the list of structures comes up, choose 1a. Then go into the BUILD menu & choose EDIT STRUCTURE. Choose Cl from the right-hand menu & add at the appropriate places. (I.e. Click on the yellow atom at the end of the C-H bond. This will replace the yellow hydrogen with an orange chlorine.) Choose MINIMIZE. Then in the FILE menu, choose SAVE AS, for example, 1aCl and then QUIT. Go to the SETUP menu & setup & submit the AM1 geometry optimization. Check the output. Repeat for 1bCl & 1cCl.

Construct 2a using the above techniques. You will need to use the procedure for rotating atoms around a bond to change the dihedral angle (Double click on bond...as described above) in order to get the alternating pattern of single & double bonds right in the 6-membered ring. When you connect the last two atoms to make a BOND, note that you can only connect a single bond to a single bond or a double to a double--never a double to a single. Also, be careful to get the H-O-C-N dihedral angle to be cis rather than trans.

The energy is very sensitive to the geometry. The trans conformer is a local minimum rather than the global energy minimum. To check this you could run an AM1 geometry optimization using the trans conformer as a starting structure & compare the energy to the optimization run from the cis conformer as starting structure: i.e. rotate the H atom around the C-O bond to get the cis conformer. Check the dihedral angle with the GEOMETRY..DIHEDRAL command. If it is not zero degrees, set it to zero & save molecule as cis conformer.

To calculate the dipole moment of 2a, first run the AM1 geometry optimization & check the final heat of formation. Then go back to the SETUP menu, choose PROPERTIES & click on DIPOLE. SUBMIT the job. This will run a dipole moment calculation using the AM1 molecular wavefunction of the optimized geometry of 2a. When the calculation is finished, DISPLAY the OUTPUT & look for the dipole moment. CLOSE 2a in the FILE menu. Repeat for 2b.

To do an AM1-SM2 calculation on 2a using the Cramer-Truhlar method, OPEN 2a in the FILE menu. In the SETUP menu, choose SEMIEMPIRICAL. Give an appropriate TITLE, choose AM1, SINGLE POINT ENERGY (i.e. use the previously optimized geometry; no need to optimize the geometry again), & SOLVENT (WATER (C-T)). Save the choices & SUBMIT the job. DISPLAY the OUTPUT & check the heat of formation. Repeat for 2b.