Product Information
Last update: 18 April 2007

 

Exploring Potential Energy Surfaces
with Gaussian and GaussView

Gaussian 03 contains many features which allow you to study potential energy surfaces (PES) and reactions, including the following:

  • Geometry Optimizations (Opt keyword): You can minimze molecular structures and also search for transition structures.

  • Intrinsic Reaction Coordinate (IRC) Calculations (IRC and IRCMax keywords): Locate the lowest energy reaction path from a transition structure toward the reactants and products.

  • PES Scans (Scan keyword): Vary the values of selected structural parameters within a molecule and compute the resulting energies and (optionally) optimized structures.

  • Trajectory Calculations (ADMP and BOMD keywords): Starting from initial positions and velocities of the nuclei, molecular motion is propogated through time via classical mechanics, using the electronic energy and forces. These calculations, suitable for advanced Gaussian users, provide information about how reactions proceed and product distributions, and are useful when the region near a saddle point is relatively flat.distribution of products.

GaussView provides features for setting up these calculation types and for visualizing their results, the most important of which are summarized in the following table:

Job Type GV Feature Purpose
Opt to minimum (input) Edit=>Clean Rationalize the current molecular structure using a mechanics force field.

Opt=QST2 or QST3 to transition structure (input)

File=>New=>Create Molecule Group and Add to Molecule Group Build the reactants in a new molecule group. Then add another molecule to it, copy the reactant structure and then transform it into the products. GaussView will set up the molecule specifications for the Gaussian transition structure optimization correctly. You can choose to add a third structure to the molecule group as the inital TS guess for a QST3 job. You can also use Connection Editor (on the Edit menu) to specify the corresponding atoms in the various structures explicitly.
Opt (output) Results=>Optimization Displays an energy plot of the optimization steps (check Read Intermediate Geometries in the Open dialog). Animate the optimization by clicking on the green dot in the View window toolbar.
IRC (output) Results=>IRC/Path Displays an energy plot of the points on the IRC. Animate the IRC by clicking on the green dot in the toolbar.
Scan (input) Edit=>Redundant Coordinates Specify scan variables by clicking on the appropriate atoms.
Scan (output) Results=>Scan Displays a 2D (scan over 1 or >2 coordinate(s)) or 3D (scan over 2 coordinates) energy plot of the points in the scan. Animate the scan by clicking on the green dot in the toolbar.
Trajectory (output) Results=>Trajectory Displays an energy plot of the points on the trajectory. Animate the trajectory by clicking on the green dot in the toolbar.
All File=>Save Movie
(requires GaussView 4) 		Save Molecule Group frames as an movie/animation.

The following figure illustrates visualizing the results of a geometry optimization on malonaldehyde in GaussView. The energy plot of the successive optimization steps is on the left, below the GaussView toolbar, while the molecule group containing the various molecular structures is on the right. You can click on any point in the plot, and the corresponding structure will appear. You can also animate the optimization by clicking on the green dot in the View window's toolbar (in this case, the molecule bounces around a bit before reaching the minimum)..

Optimizations
Geometry Optimization Output: Click on the molecule to view a movie of this optimization.

The results of an IRC calculation appear in the figure below. Again, the structures corresponding to each IRC point are contained within the molecule group. All of the ponts in the energy plot are again clickable.

IRC
IRC Output: Click on the molecule to view a movie of this IRC.

Here is a movie of another IRC, this time from an SN2 reaction.

The following figure illustrates using the Redundant Coordinate Editor in GaussView to set up a Scan calculation. Here, we are specifying the second coordinate to be scanned: the angle between the three central carbon atoms. Note that we have turned on labels to aid in selecting and specifying the coordinates (View=>Labels). The coordinate type is set to Scan Coordinate in the lower popup menu on the Coordinate panel.

Setting up a Scan
Setting up a Scan Calculation with the Redundant Coordinate Editor.

Here are the plot and molecule group resulting from the completed Scan calculation (we opened the Gaussian output file to view these results):

Scan
Plot and Molecule Group from a Scan Calculation.

Since this was a scan over two coordinates, the plot is a surface. The various scan points are shown on the plot, and each is clickable as usual. We have highlighted the current point in the plot above.

Note that the plot can be rotated as zoomed as desired using the usual mouse buttons. For example, here is a view of it from the other side: Repositioned Scan plot

The output results from trajectory calculations is similar to that for optimizations and IRC calculations as illustrated above.