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Visualizing Gaussian’s Results with Chem3D

Æleen Frisch, Ph.D, published in ChemNews.Com VOL 9 NO 2

Running gaussian jobs from within Chem3D Ultra is easy (as we saw in a previous issue of ChemNews.Com). This time, we’ll look at some of the ways that you can view results from Gaussian calculations visually using Chem3D Ultra.

In these examples, we’ll be assuming that the Gaussian jobs were run from Chem3D Ultra (using Gaussian W). However, since Chem3D Ultra can open cube files and formatted checkpoint files, results computed with Gaussian on other computer systems may also be visualized with Chem3D Ultra.

Basic Results

After you have initiated a Gaussian job using the items on Chem3D Ultra’s Gaussian menu, you can continue working in Chem3D Ultra while the job runs in the background. Once the job finishes, numeric results are reported in the regular Chem3D Ultra Messages window.

The illustration in Figure 1 shows an example. This output comes from a single point energy energy calculation on formaldehyde using Gaussian W. In this case, the predicted energy for this molecule is about -113.2 Hartrees. The Messages window also reports the predicted dipole moment for the molecule as well as the charges on each of the atomic nuclei.

If we had performed a geometry optimization (minimization) with Gaussian instead of a single point energy calculation, the molecular structure in the other window would also have been updated to reflect the calculation’s results (the final predicted structure).

Molecular Orbitals

Chem3D Ultra also includes extensive molecular visualization capabilities, virtually all of which may be used for results from Gaussian calculations as well as ones computed by Chem3D itself. Molecular orbitals are often the first item a researcher chooses to visualize.

Any molecular orbital can be selected to be displayed byselecting Chem3D’s View=>Molecular Surfaces=>Molecular Orbitals... menu path.

Figure 1: Chem3D display of numeric results from a Gaussian Calculator

This selection brings up the Molecular Orbital Surface dialog box:

The Orbital scroll list allows you to select the molecular orbital (MO) that you wish to view. By default, alpha (positive) nodes are colored red and beta (negative) nodes are colored blue. However, you can select other colors by double clicking on either color box. The Isocontour field specifies which MO isodensity surface is displayed (the default value seldom needs to be changed). The Grid area specifies the number of points in the numerical integration computation of the surface, with more points corresponding to a sharper contour edge (and a correspondingly longer surface computation time).

Clicking the Show Surface button causes the requested MO to be computed and displayed (the button then changes to Hide Surface). Here is the highest occupied molecular orbital (HOMO) for formaldehyde, which happens to be orbital number 8:

The Surface Type pop-up menu allows you to specify the way that the surface appears when it is displayed. The preceding example showed a solid (opaque) surface. The other options are displaying the surface as a series of dots, as a wire mesh and as a transparent surface. Here is the same orbital displayed in the latter mode:

Here is the LUMO for formaldehyde, plotted in the same manner (we have rotated it slightly to expose the lobes in the back more clearly):

Other Surfaces

Other types of surfaces can be visualized in a similar manner.The various items on the View=>Molecular Surfaces submenu are used to specify the type and parameters of the desired surface (see Figure 2 below).

For example, here is the electrostatic potential surface for formaldehyde:

The red node indicates the areas of positive electron density, and the blue node indicates the areas of negative electron density.
Figure 2. The Molecular Surfaces submenu.

Ultraperties Mapped onto a Surface

Chem3D Ultra also has the ability to plot one molecular Ultraperty onto another surface computed for the molecule. For example, we can map the electrostatic potential onto the charge density surface: the value of the electrostatic potential at each point on the charge density surface determines the color of the surface at that point.

Such a plot is specified with the Total Charge Density Surface dialog box:

The Map Ultraperty pop-up menu indicates which Ultraperty is to mapped onto the charge density surface (one of its choices is None, indicating that only the charge density surface itself is to be plotted).

Here is the plain charge density surface for acrolein, displayed in wire mesh mode:

We can see the acrloein molecule within the charge density surface.

Figure 3. The electrostatic potential mapped onto a charge density surface for acrolein.

Figure 3 shows the electrostatic potential mapped onto this surface. The range of values for this parameter are displayed as the spectrum of colors from red (highest positive) to violet (greatest negative), with intermediate colors indicating regions of values in between these extremes.

These examples represent just the simplest ways that Gaussian and Chem3D Ultra can be combined to predict chemical Ultraperties and structures. We will consider more advanced capabilities and techniques in future issues.

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