ESP Maps

Isodensity surfaces colour-coded with the electrostatic potential can be used to produce qualitative insights into a number of different chemical situations. This article shall refer to these as "ESP maps", although this term is less accurate it is certainly a lot easier to say. The software used is Gaussian and VMD, although the process is similar for a number of different packages and visualisers.

Gaussian cube files

The first step is to obtain the isodensity and electrostatic potential information.

Add %Chk=foo.chk to the Gaussian input file.

Using the formchk utility: formchk foo.chk foo.fchk

Create a cube file containing the density information: cubegen 0 density foo.fchk foo-dens.cube 80

And a cube file containing the electrostatic information: cubegen 0 potential foo.chk foo-esp.cube 80

VMD

The following guide is purposefully vague as producing images is a creative process:

Open the density cube as a new molecule.

Open the ESP cube as data for the existing molecule.

In Graphics/Representations, change the drawing method to Licorice.

Create a new Represenation, with a drawing method of Isosurface.

Change Draw to Solid Surface.

Change Show to Isosurface.

Adjust the isovalue to personal preference. 0.04 is a decent starting point.

Change the Isosurface coloring method to Volume, selecting the ESP cube in the adjacent box.

Adjust the color data range under the Trajectory tab.

A color scale bar can be added through the Extensions menu.

With some further adjustments you can end up with an image that looks something like this:

Some settings

Some of the settings below have worked well for us.

Colors: An RWB color scale with a midpoint of 0.50 to 0.65.

Material Settings:

Ambient = 0.30

Diffuse = 0.43

Specular = 0.25

Shininess = 0.65

Opacity = 0.69

Outline = 0.07

If you'd like to highlight a particular atom, add a new Representation and set the Drawing Method to VDW. Set the Selected Atoms to, for example, element Cu.

Under Display, you might want to select Orthographic, and adjust Cue under Display Settings.

For the final production graphic, I tend to use internal Tachyon under File/Render.