In this tutorial, we demonstrate GaussView features for visualizing Gaussian results
as three-dimensional surfaces.
We will view: molecular orbitals,
electron density surfaces, mapped surfaces,
and other volumetric data.
We begin by visualizing molecular orbitals.
To do so, we must generate surface data known as a cube, which is a volumetric data object.
Once generated, we can display a cube as a surface.
We can then go on to customize the surface display and/or display the data as a contour.
In order to visualize the surfaces, you will need to open a Checkpoint file, which has
the extension .CHK, or a Formatted Checkpoint file, with the extension .FCHK
or .FCH under Windows.
We have already opened our results file.
We select Surfaces/Contours from the Results menu, to bring up the following dialog.
It is organized into three sections.
The upper part is used to generate cube data, which can then be displayed as surfaces or
contours.
The middle section controls the display of surfaces, while the bottom section controls
the contour displays.
To begin, click the Cube Actions dropdown and select New Cube.
We want to visualize molecular orbitals, so we leave the Type menu selection as is.
The Orbitals dropdown is used to specify the desired orbitals.
Select HOMO, LUMO to generate both the highest occupied molecular orbital, and the lowest
unoccupied molecular orbital cubes in one operation.
Once both cubes are ready and available to use, we can visualize them.
At the bottom of the dialog, click the Add view for new surfaces/contours checkbox.
This option will generate a new View window for each new surface or contour.
In the Surface Actions dropdown, select New Surface.
GaussView will generate a surface from the currently selected cube.
After a moment, the generated surface appears.
This is orbital 8, the HOMO for this molecule.
Note that we previously changed the display from its default, solid, to transparent.
We will demonstrate this process later.
In order to compare this Molecular Orbital to the LUMO, select the second cube and then
display its surface.
After repositioning the two View windows, we can see both the HOMO and LUMO.
The LUMO is on the left.
The HOMO is an oxygen lone pair of electrons and the LUMO is the carbon oxygen π anti-bonding
orbital.
From the Display Format dialog, GaussView lets you change the surface’s level of transparency
with this slider.
Other options on the Format popup will display the data as a solid surface, or as a mesh.
You can also save any GaussView image as a publication-quality graphic using the File->Save
Image menu item on the context menu.
We specify the image file name, and the image format as JPG.
The toolbar Save Image icon also performs this operation.
Finally, we can display the MO as a contour within a plane using the Contour Actions dropdown.
When we select New Contour, a dialog to specify the desired contour opens.
In this case, the default contour plane happens to be perpendicular to the C-O double bond.
We can specify an alternate plane for the contour by clicking the Define Plane button
in the Generate Contours dialog.
Once the Define Plane dialog opens, the View window shows the defined contour plane.
The default plane is perpendicular to the C-O bond.
It is defined by a normal vector at the origin along the Z-Axis.
In order to create a contour in the plane of the molecule, we change the Method dropdown
to Three points, which means that we use 3 atoms within the molecule to define the plane.
This is obviously very easy for formaldehyde.
We specify atoms 2, 1 and 4, which are the oxygen atom, the carbon atom and one of the
hydrogen atoms respectively.
The plane we want is now defined.
Once we click OK, the resulting contour display appears.
If you want to visualize more than a couple Molecular Orbitals, it’s usually better to use the
MO Editor rather than generating and visualizing each one individually.
With the same formatted checkpoint file still open, we click the MO Editor button on the
toolbar, which opens the MOs dialogue.
The molecular orbitals are listed on the right in order of decreasing energy.
Virtual orbitals are separated from occupied orbitals by the dashed green line.
We want to examine MOs 5 through 10, so we select them in the list.
We navigate to the Visualize tab in the lower portion of the dialog.
The list of MO cubes to generate is specified in the Add List field.
When we click on the Update button, GaussView generates each of these displays.
The small grey boxes in the orbital list indicate that it can be viewed.
Clicking a box displays the corresponding orbital.
GaussView can also create other chemically-relevant surfaces, including mapping one property onto
another.
We open the Surfaces and Contours dialog and generate an Electron Density cube.
We choose Total Density from the Type popup and choose the SCF Density Matrix.
Once the cube generates, we add a new surface, plotting the SCF electron density.
We will now map another property, the electrostatic potential, onto this electron density surface.
We select New Mapped Surface from the Surface Actions menu.
This opens the Surface Mapping dialog.
We will generate the value of the electrostatic potential at each point, so we click the second
radio button and leave the Type menu selection set to ESP.
Once we click OK, GaussView will calculate the ESP values and color each surface point
accordingly.
The color range is defined at the top of the dialog.
The surface transparency makes it difficult to see.
To make it more opaque, we right click, select View and then Display format.
We disable the Fade mapped surface values option, making the detail clearer.
The slider at the bottom of the dialog controls the Z-Clip option.
Increasing it removes the front portion of the surface, which allows views into the interior.
We will use an analogous technique to generate and display a difference density between the
first excited state and the ground state.
First, we generate an excited state Electron Density cube.
We select the CI Density Matrix which corresponds to the excited state, which in this case comes
from a TD-DFT calculation.
Once this cube is ready, we generate a third cube using the Subtract Two Cubes option.
This computes the difference in value between 2 cubes at each point.
Cube 1 is the CI Density cube we just generated, and Cube 2 is the SCF density cube we first
generated.
Clicking OK computes the excited state minus the ground state density.
Now we want to map this new data onto the SCF electron density surface.
We make sure that the SCF Density is still selected.
Then we change the Isovalue for the surface.
Next, we select New Mapped Surface from the Surface Actions menu.
We will use an existing cube as the source of the mapped values.
Then we select the Difference Density Cube from the list.
The resulting mapped surface does not take advantage of the full color range available
to it.
Rather, it is mostly green with a bit of blue.
We can modify the color range using the values at the top of the surface display.
We want to decrease the range of the plotted data so that the entire color range is used.
We change both values from 10 to the -5 to 10 to the -6, and the resulting surface becomes
much more informative and detailed.
The blue region indicates positive values of the difference density—in other words,
where the excited state density is large than the ground state density.
Red regions indicate the reverse.
Therefore, for this molecule, electron density moves from the regions of the two rings to
the opposite end of the molecule as it transitions from the ground state to the first excited
state.
The numeric values of the surface map is displayed in the bottom left of the View window, as
you mouse over the surface.
GaussView can also display the solvation cavity
for an SCRF calculation.
We’ve already opened our results file for a Single Point Energy calculation on a conformation
of methyl lactate in methanol solution.
We can display the solvation cavity using the Results->PCM Solvation Cavity menu path.
The cavity display will open, along with a dialog for customizing it.
By default, the cavity is displayed as a series of white points.
It can also be displayed as a solid or a wire mesh.
We select the Cull Backside option to eliminate the rear part of the surface from the display.
The Color by Atom option colors the display to match the atom generating each section.
We can also lower the opacity to better view the molecule’s structure.
In our next video, we will explore the methods for viewing and customizing plots, as well as saving them as publication quality images.