Quantum Chemical Geometry Optimization and Transition States

1) From your home directory create a directory for this exercise and enter that directory:

·    mkdir qmexercise

·    cd qmexercise

2) Bring up SYBYL and sketch the following molecule (propenol):





3) Minimize the molecule with all of the default settings, except for the maximum number of iterations (use 200 instead of 100).  Take note of the final energy and save the final structure as "propenol.mol2".

4) Generate a Gaussian input deck as follows:

·  {Compute}  >>  {Interfaces}  >>  {Gaussian...}

·  Change "Geometry Optimization:" from "None" to "Full"

·  Change the "Basis Set:" to "3-21G"

·  Type in something in the "Comment:" text box (e.g., "Geometry optimization of propenol")

·  Enter a "Job Name:"  (e.g., propenol)

·  Click {OK}

5) At this point, the text window will have told you that it has written the input file "propenol.dat".  You are not going to run the job yet, though, so on the "Option" widget that pops up, click {End}.

6) Sketch the following molecule (propanal):




Note that you may find it easier just to rerun the sketcher on the propenol you sketched in step 1.

7) Minimize the propanal and then generate a Gaussian input deck in the same way as Step 3, except for substituting "propanal" for "propenol" for the  comment and job name.  Again, note the final energy and save the structure as "propanal.mol2".

8) Exit SYBYL.

9) Rename propenol.dat and propanal.dat to "propenol.com" and "propanal.com" respectively.

10) Open up a UNIX shell on the cluster via the command:

·    rsh kumgmc01

11) In this shell, cd to the directory where you created the propenol.com and propanal.com input decks. Note: your home directory on the cluster is different (/home) than your home directory on the SGI workstations (e.g., /usr/people3/b952s1), so you must use the full path to access your input directory (e.g., cd /usr/people3/b952s1/qmexercise)

12) Submit the propenol job by typing:

·  g98s propenol

13) The screen will give you a readout that looks something like:
    Current processor usage is as follows:
    ku1           up      2:06,     2 users,  load 0.02, 0.40, 0.60
    ku2           up      2:03,     0 users,  load 0.00, 0.02, 0.23
    ku3           up      2:03,     0 users,  load 1.96, 1.80, 0.04
    ku4           up      2:03,     0 users,  load 1.95, 1,81, 0.04
    ku5           up      2:03,     0 users,  load 0.00, 0.00, 0.02
    ku6           up      2:03,     0 users,  load 0.00, 0.00, 0.02
    ku7           up      2:03,     0 users,  load 0.00, 0.00, 0.02
    ku8           up      2:03,     0 users,  load 0.86, 0.34, 0.17
    Please specify a low-load processor for your job:

Look at the three last columns which are the processor "load" columns (averaged over the last minute, last 5 minutes and the last hour respectively) choose a processor with a small value for load over the past minute (e.g., in the case above ku2, ku5, ku6 and ku7 have all been inactive), type in this processor and hit the "Enter" key.

14) In a similar fashion, submit the propanal job.

15) The jobs will take several minutes to complete, at which point the output files "propenol.log" and "propanal.log" will appear on your directory.  You can use the command

·  ls *.log

to spot them as they arrive.

16) Once the output files are there you can view their contents with the command:

·  cat propanal.log

(and likewise for propenol).  First of all, check to see that the job ran correctly: the very last line of a successful run should read "Normal termination of Gaussian 98."  Next peruse and take note of some of the other output information you get from your run, including multipole moments, charges, spatial extent (related to molecular volume), orbital information, and the final optimized atomic coordinates.

17) The total energy is your calculation is somewhat buried in your output and can be hard to find.  To see this more easily, use the command:

·  grep "SCF Done:" propanal.log

and you will get back a bunch of numbers which reflect the total energies of the molecule at different steps during the geometry optimization.  The last value in this list will be your final total energy.  These energies are expressed in hartrees which can be converted to kcal/mol (1 hartree = 627.5095 kcal/mol).

18) Analyze the output from both propenol.log and propanal.log, and compare the relative energies.  Note that the total energies will bear no resemblance to those you determined in steps 3 & 7, however the relative energies can be compared.  From your SCF results, compute the heat of reaction for propenol reacting to form propanal and convert this energy from hartrees to kcal/mol.  Compare this with the heat of reaction you would predict from the simple molecular mechanics calculations (steps 3,7).  How do they differ?  Why do you think they differ?

19) Next you're going to find the transition state for the reaction of propenol forming propanal.  To do this, you will need to create a file that contains both the starting geometry for the propenol job and the starting geometry for the propanal job, looking like:
    # HF/3-21G OPT=(QST2)

    Geometry Optimization of Propenol

    0 1
       6      -8.0096951       0.6920720      -0.0557060
       6      -6.9229841       1.7384430      -0.0069330
       6      -5.6248922       1.4333850       0.1515210
       8      -4.6687498       2.3735509       0.1935450
       1      -8.7301207       0.8777330       0.7552720
       1      -7.6163831      -0.3299420       0.0554500
       1      -8.5367546       0.7593480      -1.0194790
       1      -7.2453079       2.7761090      -0.1082960
       1      -5.2990088       0.3985550       0.2527640
       1      -4.9636469       3.2736850       0.1049300

    Geometry Optimization of Propanol

    0 1
       6      -9.8537302       1.3308721      -0.5413280
       6      -8.9657078       2.4280190       0.0967940
       6      -7.5428600       2.2972870      -0.3834240
       8      -7.0096159       3.1974399      -1.0120389
       1     -10.8927994       1.4302990      -0.1895590
       1      -9.4835052       0.3305460      -0.2669700
       1      -9.8417864       1.4244860      -1.6386230
       1      -9.3647881       3.4220450      -0.1645020
       1      -6.9730101       1.3921860      -0.1740790
       1      -8.9807167       2.3281460       1.1940880

To generate this file carry out the following commands:

·  cp propenol.com transition.com

·  cat propanal.com >> transition.com

Note that the ">>" in the above command causes the contents of the file "propanal.com" to be written to the end of the file "transition.com" instead of to the screen.

20) Once you have done this, you will need to edit the input deck (i.e., vi transition.com) and make the following changes:

·  Line 1:  change "%chk=propenol.chk" to "%chk=transition.chk"

·  Line 2:  change "# HF/3-21G OPT" to "# HF/3-21G OPT=(QST2)"

·  Line 18:  delete entirely (i.e., use the "dd" command)

·  Line 19:  delete entirely

·  Line 20:  delete entirely

At this point, check over your file "transition.com" to ensure it looks basically the same as the template shown in step 19.  Minor variations in the atomic coordinates or the comment lines are fine.

21) Once your input deck is finished, save it and quit from vi.

22) Submit the transition state calculation as a Gaussian via the "g98s transition" command.

23) Analyze the resulting output in the same manner as you did for propenol and propanal.  Compute the energy difference between your transition state structure and your final propenol reaction -- this is the activation barrier for the propenol ® propanal reaction.

24) Exit from your session on kumgmc01.msg.ku.edu by typing "exit".  

25) Back on your local machine, cd to your "qmexercise" directory, fire up SYBYL again, and read in the following files:

·  read propenol.mol2 into "M1:"

·  reread propenol.mol2 into "M2:"

·  read propanal.mol2 into "M3:"

26) Import your Gaussian output files for analysis as follows:

·  {Analyze}  >>  {Interfaces}  >>  {Gaussian...}

·  For "Gaussian output file:" type in "propenol.log"

·  For "Molecule:" select "m1:"

·  Click the little button next to "Charges".  If nothing happens, click it again, and the quantum chemical charges for each atom in the propenol structure should appear.

·  Click the button next to "Energies" and the text window should give you details such as the total SCF energy, orbital energies, and the dipole moment.

·  Click the button for "Geometry" and after a few seconds, the molecule should be redrawn with the geometry corresponding to the quantum simulation.

Note:  don't click the {OK} button until you're ready to leave the Gaussian analysis widget -- this will close it prematurely.

27) Do the same for your transition state structure by importing "transition.log" into molecule "m2:", and then importing "propanal.log" into "m3:"

28) Compare the relative charges on the atoms of the different structures.  If you have trouble remembering which structure corresponds to which molecule, you may wish to color each of the three structures a different color with the:

·  {View}  >>  {Color}  >>  {Atoms...}

Command (remember to specify which molecule you want to color and specify "All" atoms for that molecule).

29) Compare the dipole moments for the three structures.  Why do you think the propanal has the largest dipole moment?  (Hint: note the changes in atomic charges).



David Johnson
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