Viewing a Reaction Path with GaussView

(GaussView Version: 3.09)

 

 

 

Gaussview can be utilized to view the reaction pathway.  The program reads the formatted checkpoint file or the output file from a Gaussian calculation.  This example looks at the reaction pathway of H₂ and acetone.

 

 

Generating Formatted Checkpoint Files

 

When running the Gaussian calculation there are two ways in which you can get the desired formatted checkpoint file.

1.      As a keyword, enter formcheck.   This will create a .FChk file when the Gaussian calculation is complete.

2.      After the Gaussian calculation is complete, open Gaussian.  Select Utilities|FormChk.  In the dialog box that appears, browse for the checkpoint file that was previously created.  Select it.  This will create a formatted checkpoint file with the extension .fch that has the same name as the checkpoint file.  (This is the preferred method.)

 

 

Preparing to Visualize Reaction Path

 

• Create reactants, products, and an educated guess at the transition structure
• Run these through a Gaussian optimization job
• Use additional keywords opt (QST3, CalcFC)
• QST3 is a search for a transition structure
• This option requires the reactant, product, and initial transition structure structures as input
• CalcFC specifies that the force constants be computed at the first point
• Create a formatted checkpoint file
• Next, run these through a Gaussian frequency job
• Create a formatted checkpoint file
• Finally, run these through a Gaussian Reaction Path job (IRC)
• Use additional keywords IRC (Maxpoints=24, RCFC, phase=(1,2)) NOSYMM 
• IRC requests that a reaction path be followed
• Maxpoints represents the number of points along the reaction path to be examined
• RCFC specifies that the computed force constants in Cartesian coordinates from a frequency calculation be read from the checkpoint file
• Phase defines the phase for the transition vector
• If two atom numbers are given, the coordinate is a bond stretch between the two atoms
• Create a formatted checkpoint file

 

Note:  IRC Calculations require initial force constants to proceed.  These must be provided to the calculation in some way.  The usual method is to save the checkpoint file from the preceding frequency calculation (used to verify that the optimized geometry to be used in the IRC calculation is in face a transition state).

 

 

Visualizing Reaction Paths in GaussView

 

• Select File|Open.  Select either the formatted checkpoint file or the output file that was created from the IRC Calculation.  Select OK.
• A window will appear with the selected structure displayed with the option of showing all the steps along the reaction pathway.
• The formatted checkpoint file will have 1 of 49 steps of the reaction pathway
• The output file will have 1 of 48 steps of the reaction pathway

 

 

 

• To view each of the steps along the reaction pathway, simply click on the up or down arrow located next to the first number.
• To view a timeline of all the steps along the reaction pathway, click on the button that shows a split screen with two molecules located next to the second number (the one that is fixed).  The button will now only show one molecule.  To view only one step at a time, click on the same button.
• To view a slideshow of all the stops along the reaction pathway, click on the green button located next to the first number.  The green button will turn into a red “X”.  To stop the slideshow, click on the red “X”.

 

 

 

 

TIPS:

• To rotate the molecule, click in the main window and move the mouse while holding down the left button.
• To enlarge the molecule, hold down the Control key and move the mouse while holding down the left button.
• To translate the molecule, hold down the Shift key and move the mouse while holding down the left button.

 

This page written by Jeremy Beck and Rachel Fogle, York College of PA

 

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