It actually works!

So I fooled around with Gaussian, doing some transition state and IRC calculations for the conversion of HCN to HNC via hydrogen migration. The first step was determining the transition state of the reaction (reaction path calculations start at the transition state and travel in both directions around it). For this I used Gaussian’s QST3 option, listed under transition state optimizations in GaussView. This required three molecules: the starting material, the product, and a transition state guess. Optimizing the starting materials and products to minima before running QST3 is advised, as is running an opt+freq QST3 job so the force constants of the optimized transition state can be used in a calculation of the reaction path. You can also use the frequency results to verify that the optimized structure actually is a transition state (although Gaussian usually yells automatically if it isn’t).
Running the QST3 job gives a single molecule as output, the optimized transition state. I copied this structure into a new input window and set things up for an IRC calculation by first selecting IRC under Job Type and then specifying that Gaussian should read force constants and a geometry guess from the transition state’s checkpoint file. Click the picture to enlarge.
I ran the calculation, and voila! Under Results->IRC there was a nice little video of the hydrogen moving from C to N, along with a graph of energy versus reaction coordinate. Input files for both steps are shown below.

Advertisements

2 Comments

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s