How to use RNBO to generate claisen rearrangement

How to use RNBO to generate claisen rearrangement

Postby jwkeller » Fri Mar 29, 2019 7:16 pm

The NBO 7 manual is not at all clear on how to go about generating the reacting orbitals, and changing conformations, as shown in the movie. If I can understand that, then I may be able to apply it to my own situation. It must require many calculations, one at each reaction stage, then creating an animated .gif from about 100 screen shots.
John Keller
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Re: How to use RNBO to generate claisen rearrangement

Postby ericg » Mon Apr 01, 2019 11:10 am


You're correct; a large number of calculations are required to produce an animation for a chemical reaction. The steps are essentially the following:

1. Optimize the transition state, and calculate the forward and reverse intrinsic reaction coordinate (using a smaller than default stepsize). Ideally, the IRC should generate 40-80 geometries across a significant portion of the reaction surface.

2. Perform NRT/RNBO analysis at each geometry along the IRC, produce a digital image of the desired RNBO at each geometry, and concatenate the images into an animated GIF file.

We use scripts to automate portions of the Gaussian/NBO/NBOView effort. But it still takes a couple of weeks for a student to complete a single animation.

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