Note: The discussion of antiferromagnetic coupling in the G03 Tips & Techniques section also includes a useful GaussView example of building a molecule with very high symmetry (D2h in this particular case).

Setting up QST2 jobs in GaussView:
A Foolproof Technique for Achieving Identical Atom Ordering

Gaussian 03's Opt=QST2 and Opt=QST3 features are very useful for automating transition structure searches for a given set of reactants and products (and TS initial guess in the case of QST3). In order to use these features, you must provide G03 with multiple molecular structures with the atoms specified in the same order in all of them. GaussView makes it easy to achieve this. The procedure is described below using an SN2 reaction as an example:

  1. Draw the reactants in a new Molecule Group:

  2. Choose Edit → Copy.

  3. Choose Edit → Paste → Add to Molecule Group. This will cause the reactant structure to be added to the Molecule Group as a second molecule. The window will now look like this:



    At this point, you may view both structures in side-by-side panes by clicking the View Both button (a toggle) in the toolbar:

  4. Modify the structure of molecule 2, using the normal GV tools (e.g. bond distance, bond angle, and dihedral angle), in order to transform the reactant structure into the product structure:



    As long as you do not add or remove atoms, the atom ordering will remain the same.

  5. Choose Calculate → Gaussian to set up the job. In the Gaussian Calculation Setup dialog box, select the Job Type tab and choose Optimization from the drop-down list. In the Optimize to a drop-down list, choose TS (QST2). The window will now look like this:

Additional Notes:

  • You can view the atom numbers by choosing View → Labels to manually verify that the ordering is the same.

  • To set up atom equivalencies manually, use the Connection Editor in the Edit menu (see GaussView manual for details).

  • To optimize products and reactants separately before running a QST2 transition structure optimization, cut and paste each structure into its own new Molecule Group. Then optimize the individual molecules, open the Results file in GaussView, and copy & paste each optimized structure back into the original Molecule Group, replacing the original unoptimized structure you created. This technique works because atom order is maintained throughout the individual optimization.

Building Polymers

There are many different strategies for building polymers with GaussView. Here is one recommended by the Gaussian tech support staff. It uses neoprene as an example:

  1. Start by building the monomer:



    Look at the C-H bond between the fourth carbon and the hydrogen that is in the same plane as the carbons. We will now prepare the monomer to become a polymer by adjusting what will become the intercell bond. Change this C-H bond length to be that of a typical single C-C bond (e.g. 1.54 Å). You must modify this length because this H is the one to be replaced by the next monomer unit in your polymer. The above illustration shows the monomer with the modified bond length.

  2. Choose Edit → PBC, and select the Symmetry tab in the resulting dialog box. In the Lattice Dimensions drop-down list, choose One to create the translation vector. The window will now look something like this, with the translation vector appearing in red:

  3. To place the vector in the proper position, select the Cell tab, and in the lower section click Place. In the Vertex drop-down list, choose O(0), and in the Location drop-down list, choose Atom. The dialog box will now look like this:



    Then click on the desired atom in the diagram, in this case the leftmost carbon. Go back to the dialog box and change Vertex to a(1) and click on the hydrogen on the rightmost carbon. You have just defined the polymer's unit cell, as shown below:

  4. We now need to delete the hydrogens that will be replaced by carbons in the polymer. One way to do this is to use the Trim Contents drop-down list (also in the Cell tab) and select Delete All Atoms Outside Cell. Alternatively, you can delete the appropriate atoms by hand.

    Here is the final unit cell for neoprene:

  5. In order to view multiple unit cells, select the View tab, and in the Cell Replication drop-down list, choose as many units as you wish to view. In our example, we chose 3 (and we also set Replicate Contents Display to High Layer):



    If some bonds are missing from the display, select the Contents tab, and choose Rebond All from the Bonds drop-down list.

    At this point, you are ready to set up your Gaussian 03 PBC job.

Retaining Additional Information in Your Gaussian Input File

When running GaussView, there may be occasions where you open a Gaussian input file which has some extra information in it (for example, extra basis functions have been specified). You may work with your file within GaussView, setting up different jobs, etc., but care must be taken when you wish to save the file so that this extra information is not lost. However, it's easy to save the extra information by following the procedure described below:

When you submit the job, GaussView asks if you want to save the file. You must check the box Append Extra Input at the bottom of the Save dialog box (shown highlighted below):

If this box is not checked, the extra information will be stripped out (i.e. not saved).