Viewing Gaussian Difference Densities with GaussView

Viewing Gaussian Difference Densities with GaussView

(GaussView Version: 3.09)

Download The Files Associated With This Example
Ground State Input File Output File Cube File
Excited State 2 Input File Output File Cube File
Excited State 3 Input File Output File Cube File

Gaussview can be utilized to view the total electron density difference between ground and excited states.  The program reads the formatted checkpoint file or the cube file from a Gaussian calculation.  This example looks at several of the excited states of acrolein.

Generating Cube Files

  • For a Ground State Density
    • CIS/6-31G(d) density(SCF) cube=density NoSymm
    • At the end of input information
      • Blank line > filename_gs.cube > Blank line
  • For an Excited State Density
    • Input information located directly below last blank line from Ground State Density input information
      • –link1–
      • %chk=filename.chk
      • # geom=allcheck guess(read, only) density(checkpoint,cis=n) cube=density

NoSymm

        • Where n represents the number for the excited state (example: n=2 for the second excited state)
      • Blank line > filename_ex.cube > Blank line

Note:  There are numerous ways to generate cube files.  The method instructed above is simply the way chosen for this particular demonstration.  Also, the NoSymm keyword is included to ensure that Gaussian does not reorient the molecule between calculations due to symmetry. If this occurs, the cube files could have different coordinates and not line up properly when viewed.

Creating Difference Density Cube Files in Gaussian

  • Select Utilities|CubMan.  A small window will appear.
  • Enter “su” for subtract at the initial prompt
    • This operation subtracts two cube files to produce a new cube file.
  • For the first input file type the name of the excited state cube file (example:  filename_ex.cube)
    • Is the file formatted?  Answer “y” for yes.
  • For the second input file type the name of the ground state cube file (example:  filename_gs.cube)
    • Is the file formatted?  Answer “y” for yes.
  • For the output file type in the name desired for the difference density output file (example:  filename_diffex.cube)
    • Should it be formatted?  Answer “y” for yes.

Follow the above procedure for each of the excited states that you want to visualize the difference densities for in GaussView.

Generating Formatted Checkpoint Files

When running the Gaussian calculation there are two ways in which you can get the desired formatted checkpoint file.

  1. As a keyword, enter formcheck.   This will create a .FChk file when the Gaussian calculation is complete.
  2. After the Gaussian calculation is complete, open Gaussian.  Select Utilities|FormChk.  In the dialog box that appears, browse for the checkpoint file that was previously created.  Select it.  This will create a formatted checkpoint file with the extension .fch that has the same name as the checkpoint file.  (This is the preferred method.)

Visualizing Difference Densities in GaussView

GaussView can be used to read in two formatted checkpoint files or two cube files, take the difference, and create an isosurface rendering of the result.

  • Select File|Open.  Select the formatted checkpoint file for the excited state that you want to visualize the difference density for in GaussView.  Select OK.
  • Select Results|Surfaces.  A Surfaces and Cubes window will appear.
  • Select the Cube Actions drop down menu.  Select Load Cube.  Find the cube file that represents the difference density calculated with CubMan.  Select OK.
    • A line of data will appear in the Cubes Available box.
  • Select an appropriate isosurface value (such as 0.004)
    • Adjust the isosurface value until you obtain a visualization of the difference densities that is ideal.
  • Select the Surface Actions drop down menu.  Select New Surface.
    • A line of data will appear in the Surfaces Available box.
    • This will generate a graphical window with the molecule and difference density for your excited state.
      • The blue represents where the electrons are coming from, and the purple represents where the electrons are going.
    • If the visualization is not ideal, select the Surface Actions drop down menu.  Select Remove Surface.  Change the isosurface value.  Select the Surface Actions drop down menu.  Select New Surface.
      • Repeat these steps until the visualization for the difference density is ideal.

Acrolein Difference Density (Excited State 2 and Ground State) – Viewed in GaussView

Acrolein Difference Density (Excited State 3 and Ground State) – Viewed in GaussView

TIPS:

  • To rotate the molecule, click in the main window and move the mouse while holding down the left button.
  • To enlarge the molecule, hold down the Control key and move the mouse while holding down the left button.
  • To translate the molecule, hold down the Shift key and move the mouse while holding down the left button.

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