Goals of this Exercise
Optimization of the (H2O)2 molecule using PM7 method (you can also use other method and other computational chemistry software)
Computing of the electronic density.
Doing a 2D NCI analysis
Computing and showing the NCI iso-surface.
Detailed Instructions
Building of the Molecule
Click on Draw/Display Geometry icon
On Drawing Area click with right button
of the mouse and select Add/Fragment.
Select Water molecule,
Click on the H atom (right window)
Click to Drawing Area.
Click a second time to Drawing Area click
Click to the « measure » icon.
Select the to Oxygen atoms.
Set the distance to 2.5
You have successfully built the
desired structure.
Optimizing the Molecule using PM7 method
1) Close Geometry Windows.
2) Choose File/New Mopac input (or Mopac icon) from the principal Menu.
3) Select Equilibrium structure search.
4) Click OK button.
5) Click to Run icon (toolbar, top of window).
6) Select your folder
7) At save data file in text zone , �type testNCI
When the job completes : click to “Display icon” button
On Drawing Area of Geometry/Display window click with right button of mouse and select Orbitals/Read geometry & orbitals from Moapc aux file and select testNCI.aux file.
Click to “O” button (toolbar at the left of the Drawing window)
Click to close button of the right window.
Click on Geometry/Display window using the right button of mouse and select Density/Electronic
Set the Minimu value to -6 and the number of points to 200.
Click to Ok button
Click to cancel button of the
Isovalue window
2D analysis
Save the electronic density : Click on Geometry/Display window using
Cube&Grid/save. Set the name of file to testNCI.gcube
2D analysis
Click on Geometry/Display window using the right button of mouse and select
NCI/2D analysis
Click to OK button of the new window
NCI isosurface
Click on Geometry/Display window using the right button of mouse and select
NCI/Compute NCI surface
Click to OK button of the new window
Set the min value in -0.05 and the max to 0.05
Click to the Ok button
Set the isovalue to 0.6 and click to OK
NCI isosurface colorcoded
Right button + Cube&grid/load gabedit cube file
And select testNCI.gcube
Right button + Cube&grid/multiply by the sign of ….
Right button + Cube&grid/save in sign.gcube
Right button + Cube&grid/load gabedit cube file and select testNCI.gcube
Right button + Cube&grid/color mapping and select sign.gcube
Set the min value in -0.03
(type on Enter key of your keybord)
and the max in 0.03
Right button + reset isovlue to 0.8