Ghemical-GMS/GTK-GAMESS tutorial

Ghemical-GMS/GTK-GAMESS tutorial

Calculating energy difference between axial and equatorial methylcyclohexane at the AM1 level of theory


Assumes Ghemical-GMS 1.01.06 (released July 13, 2005) or later


By Jan H. Jensen

Department of Chemistry

University of Iowa

http://www.uiowa.edu/~quantum


It is a good idea to read sections 2.1.1-4 in the Ghemical manual before you start.


1. Build and minimize cyclohexane

1.1, Start a new molecular mechanics project (File – New Project – Molecular Mechanics)

1.2. Build the ring

1.3. Add hydrogens

1.4. Minimize the structure

1.5. Save as “cyclohexane.gpr”


2. Build equatorial methylcyclohexane

2.1. Change an equatorial hydrogen to carbon (select “draw” and click on atom)

2.2. Add hydrogens

2.3. Minimize

2.4. Save as “eqcyclohexane.gpr”


3. Optimize the geometry at the AM1 level of theory using GAMESS

3.1. Go the “Gamess input” menu

3.2. Select “equilibrium geometry” and “AM1”

3.3. Select “review” and add the following line (note the blank space in front the $ sign),

$STATPT NSTEP=50 $END

then select “keep”

3.4a. Select submit (this assumes you have installed GTK-GAMESS and GAMESS)

3.5a. Save the file as eqcyclohexaneAM1.inp (hit OK)

3.6a. Select “start”


3.4b. Select save (if you have not installed GTK-GAMESS

(3.5b. Optional: transfer your input file to another computer)

3.6b. Run GAMESS using a line command


4. Repeat for axial methylcyclohexane

4.1. Select “notebook mode” from Windows menu

4.2. Open cyclohexane.gpr (File menu)

4.3. Repeat Step 2 for axial methylcyclohexane

4.4. Go the “Gamess input” menu

4.5. Select “Review” then “Discard” (This clears the memory of the previous run)

4.6. Repeat steps 3.2. – 3.6. for axial methylcyclohexane


5a. Calculate the relative energy

5a.1. Start new molecular mechanics project

5a.2. Import eqcyclohexAM1.log (using the import button) and scroll to the end of the bottom window.

5a.3. The last energy should be -40.080559 (the energy is in units of hartrees and may be different in the last few decimal places).

5a.4. Repeat for axcyclohexAM1.log to find the energy -40.078297

5a.5. Subtract the energy of the equatorial conformer from that of the axial, and multiply the results by 627.51 kcal mol-1/hartree. You should obtain 1.4 kcal/mol with the equatorial form being lower, which is in good agreement with the experimental free energy difference of 1.7 kcal/mol at room temperature.


5b. Calculate the relative energy using MacMolPlt (http://www.scl.ameslab.gov/~brett/MacMolPlt/)

5b.1. Start MacMolPlt

5b.2. Open eqcyclohexAM1.log (File:Open)

5b.3. The energy at the bottom of the window should be -40.0806 (the energy is in units of hartrees and may be different in the last decimal place).

5b.4. Repeat for axcyclohexAM1.log to find the energy -40.0783

5b.5. Subtract the energy of the equatorial conformer from that of the axial, and multiply the results by 627.51 kcal mol-1/hartree. You should obtain 1.4 kcal/mol with the equatorial form being lower, which is in good agreement with the experimental free energy difference of 1.7 kcal/mol at room temperature.


Orbitals, densities, and normal modes can be displayed using other “back-end” programs such as MacMolPlt or third-party programs such as MOLDEN.


See also a list of suggested GAMESS keywords for large molecules.



Select Screen-shots:


1. Build and minimize cyclohexane



2. Build equatorial methylcyclohexane


3. Optimize the geometry at the AM1 level of theory using GAMESS




4. Repeat for axial methylcyclohexane


5a. Calculate the relative energy

5b. Calculate the relative energy using MacMolPlt (http://www.scl.ameslab.gov/~brett/MacMolPlt/)