Using a mixture of basis-sets and psuedo-potentials

Important Carry out this calculation on the HPC.

Create a Molecule of BBr3

  • when compunds contain both heavy atoms which require a pseudo-potential, and light atoms, which are treated more accurately with a full basis set we need to be able to mix psueod-potentials and basis sets.
  • Set up a calculation for BBr3: Part1
    • open your 6-31G(d,p) optimised log file for BH3
    • open the periodic table and select Br
    • then select "atom" Br
    • now click on each of your H's in turn, they should turn into Br's with longer bonds
    • then goto "gaussian set-up calculation"
    • select "optimisation" under the "Job Type" tab
    • add a descriptive title
    • under the methods tab on the basis button choose "GEN". This switches on the option to specify basis sets for each atom individually
    • in the additional keywords section add pseudo=read gfinput. This switches on the option to specify pseudo-potentials for each atom individually and it turns on a printing option that is very useful if you make a mistake.
    • note that some of the lab computers are set up automatically to add as a default the command: "integral=grid=ultrafine" if you don't see this in your file then please add this text to the "additional commands" section. This command improves the integration of the electron density and provides a more accurate result.
    • then save your file, but do not submit it, ie press the submit option, save the file and then give no for the actual submission
    • close the file

      • gv_mixed_basis_and_pp

  • Set up a calculation for BBr3: Part2
    • now you need to add some information directly to the file (this is an advanced technique which gaussview does not support yet!)
    • open the .com file you have just created
    • go to the results tab and select view file, a window should open with your input file ready to edit.
    • your file should look something like this: 

    %chk=bbr3_opt_mixed.chk
# opt b3lyp/gen geom=connectivity pseudo=read gfinput
  integral=grid=ultrafine

BBr3 mixed pseudo-potential and basis set optimisation

0 1
 B                  0.00000000    0.00000000    0.00000000
 Br                 0.00000000    2.02000000    0.00000000
 Br                 1.74937123   -1.01000016    0.00000000
 Br                -1.74937123   -1.01000016    0.00000000

 1 2 1.0 3 1.0 4 1.0
 2
 3
 4

    • Now we need to specify the basis sets for all atoms and the pseudo-potential for the Br atoms. This is done after the coordinates and connectivity information. I have an example below for the BBr3 molecule where I want a full basis set on the B but PPs on the Br atoms:

    %chk=bbr3_opt_mixed.chk
# opt b3lyp/gen geom=connectivity pseudo=read gfinput 
  integral=grid=ultrafine

BBr3 mixed pseudo-potential and basis set optimisation

0 1
 B                  0.00000000    0.00000000    0.00000000
 Br                 0.00000000    2.02000000    0.00000000
 Br                 1.74937123   -1.01000016    0.00000000
 Br                -1.74937123   -1.01000016    0.00000000

 1 2 1.0 3 1.0 4 1.0
 2
 3
 4
  
B 0
6-31G(d,p)
****
Br 0
LanL2DZ
****

Br 0
LanL2DZ

    the general format is the following:

    coordinates
    (blank line)
    atomic symbols (space) 0 (zero)
    normal basis set
    **** (four stars)
    atomic symbols (space) 0 (zero)
    pseudo-potential basis set
    **** (four stars)
    (blank line)
    atomic symbols (space) 0 (zero)
    pseudo-potential
    (blank line) important!

    • add the extra information required into your file
    • save your file in the text editor, close the text editor
    • submit your job on the scan server. Instructions for submitting a file to the Scan servers.

Check that your optimisation of BBr3 has been succesful

  • Visualise the final log file in gaussview to ensure it "looks" right, none of the atoms have dissociated or strange bonding patterns have emerged.
  • Check the "Summary" data is everything as it should be? Check the method, the basis-set, the symmetry and the gradient.
  • Confirm that your optimisation has worked opening the .log file and checking the "Item" table, does each line say "YES".
  • ONLY if your job has converged properly deposit the final optimised BBr3 file in the chemical database "D-space". Instructions for adding a file to DSpace and including a link on your wiki.

Update your wiki

  • Link to your completed B3LYP/6-31G(d,p)LANL2DZ BBr3 optimisation file on your wiki
  • Include the "summary" table in your wiki
  • Include the "Item" table in your wiki
  • Include a Jmol image of your optimised geometry in your wiki
  • use the inquiry button to determine the optimised B-Br bond distance and the optimisd Br-B-Br bond angle, put this information in the table we created earlier on your wiki
  • Here is an example of my progressing wiki page.
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