Quantumchemistry, NWI-MOL406, Computer exercises, week 4 (7-Dec-2012)

Graphical user interface: ECCE - Extensible Computational Chemistry Environment

Getting started

Starting ECCE

ecce

source ~/ecces
ecce

The Builder/viewer

• First carefully read the Help information on the builder. A local copy of the help files start when you click "Help [on builder]". You can also use the online help
• Construct Fluorobenzene:
  • Click the "Import from Structure Library"
  • Select "SimpleStructures" - "Simple_arenes" - Benzene
  • Make sure you are in the "Mode: Add Structure" (upper left of work area)
  • In "Tools" make sure to select "build"
  • In the build panel on the right click on "F" (Fluor)
  • In the work area (which should now be in Atom - mode), substitutue a H atom by F
  • In the work area use the right mouse button to rotate the molecule (or select the rotate button in the menu).
  • Use the mouse wheel to zoom in
  • In "Tools" select "Atom Table" to see a table of the Cartesion coordinates
  • In "Options" select "Atom labels" - "Elements with numbers"
  • Save the cartesian coordinates to a file using "File - save as", and in the menu with formats select the last one (*.xyz). Leave "Angstroms" when prompted.

Single point SCF calculation for benzene

• To ereate an input file for NWChem, first copy the .xyz file to "benzene.nw"
• The first two lines contain the number of atoms and a title, these are not needed by NWChem. Replace them with the keywords

  start
  Geometry
  

• Complete the input with the following:

  end
  basis
     * library sto-3g
  end
  dplot
     TITLE Benzene
     vectors benzene.movecs
     LimitXYZ
     -4.0 4.0 15
     -4.0 4.0 15
     -4.0 4.0 15
     spin total
     orbitals view; 1; 7
  end
  ecce_print benzene.ecce
  task scf
  task dplot
  

• Read the NWChem DPLOT documentation to find out what this input means
• Run nwchem with this input

Analyse the fluorobenzene orbitals

• Use File - Import calculation from output file
• In the left panel read the "Calculation Summary"
• Select "Dipole Moment". Click on the "show axis" button to see if the dipole moment is pointing in the way you would expect for Fluorobenzene
• Click on "MOs". Select an MO and click on "Compute"
• Look at the orbital energies - how many core orbitals are there, and how many valence
• Plot several MOs in this way and try to find the Huckel pi-MOs.
• Which MO is the lowest pi-orbital?
• Select MO #2, use the button right of "Compute" and scroll the value of the contour up and down to find out on which atom this MO is located.
• Click the "View Coeff" button to see if you got it right (use Options to label the atoms).

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