Pentanediol for Gaussian using Nanocad & CSD

Owned by Eroma Abeysinghe
Last updated: Jul 19, 2018
3 min read
  1. Login to SEAGrid desktop client.
  2. Select Nanocad editor

    Image I - Desktop client home. Select Nanocad

  3. After NanoCAD has launched, take your time to read the text "Summary of NanoCAD Commands" at the top of NanoCAD window (Indicated by the green box in Image I). 
    1. You will get the basic idea how to use NanoCAD.
    2. Click 'Clear' to remove the existing water molecule.
    3. Click 'Structure'.

      Image II - Nanocad editor, clear the water molecule

  4. From 'Import Structure' click Database and then select CSD.

    Image III - Select CSD to search for a new molecule

  5.   Search for ‘pentanediol’ (This would take about 20 seconds). From the list given, double-click on the second one ‘anti-2,4-Diphenylpentane-2,4-diol’.

    Image IV - Pentanediol search results in CSD search

  6. The complex will get ported into the Nanocad editor. Break the C bond between the highlighted atoms. Then select ‘Group’ and do ctrl+alt+click on the C atom (Highlighted in the image) of Phenyl. Then once the group is highlighted, click ‘Clear’ and remove the phenyl molecule.

    Image V - anti-2,4-Diphenylpentane-2,4-diol complex in Nanocad editor

  7. Similar to above remove the bind between the highlighted Cs and then remove the highlighted phenyl molecule similar to above.

    Image VI - anti-2,4-Diphenylpentane-2,4-diol complex with removed atoms

  8. Ctrl+click on the gray background area to center the molecule. You can rotate the molecule by click and drag.

    Image VII - Pentanediol acid

  9. Click 'Add H' button – on the lower righthand corner.

    Image VII - Add H to the molecule

  10. Import the molecule as a Gaussian input

    Image VIII - Importing as  Gaussian input

  11. Read and say OK, to the confirmation and warning message.



    Image IX - Confirmation and warning messages on exporting molecule.

  12. Above input file is then exported into Gaussian Editor GUI. Add the Methods and Wavefunction.
     
    Image X - Add Method B3LYP & Wavefunction

  13. Add Basis set

    Image XI - Add Basis set

  14. Add Job Type

    Image XII - Add Job type

  15. Add Keywords, 'Common Keywords' → Pop and from the pop-up window select 'Reg' and click 'Done'. From 'Other Keywords' select GFInput, GFPrint and IOp. From IOp window add Overly=6, Option=7 and Value=3 click 'Done' on both windows.
        
    Image XIII - Adding Keywords to the Gaussian input

  16. In Gaussian GUI add
    1. %nproc - 16
    2. %mem - 3000
    3. Checkpoint File - Pentane23diol
    4. Check Use #P
    5. Add job title and Description - Pentane23diol #P RB3LYP/cc-pVDZ Pop=(Reg) GFInput GFPrint Iop(6/7=3) Opt Freq
    6. Charge - 0
    7. Multiplicity - 1
  17. Now 'Done & Export'.

    Image XIV - Final configurations in Gaussian GUI

  18. In the Create Experiment window
    1. Provide an experiment name
    2. Select comet.sdsc.edu to run the job
    3. Choose 'Shared' queue
    4. Submit