Move Along the Imaginary Vibration! [as a last resort for IRC calculation]

Share This:

We have published an article on our website that summarizes solutions for when IRC calculations do not work.

In the previous article, we suggested changing the algorithm or using GRRM as solutions. However, that may not work in some cases…

The last resort for IRC problem is to manually move the structure along with the direction of imaginary vibration and then optimize the structure.

Moving the structure in the direction of imaginary vibration is easy if you really understand the gaussian’s log file, but it may be difficult for others.

In this article, we will show you how to do it!

日本語版虚振動に沿って動かせ!【IRC最後の一手】

see also : when IRC calculations do not work.

Freq calculation of TS structure

First, prepare the TS freq calculation log file. In general, you probably specify the freq keyword together with opt=ts.

As an example, we pickup the TS3 strucutre from the article below.

“Enzyme-catalysed [6+4] cycloadditions in the biosynthesis of natural products”
Zhang, B.; Wang, K. B.; Wang, W.; Wang, X.; Liu, F.; Zhu, J.; Shi, J.; Li, L. Y.; Han, H.; Xu, K.; Qiao, H. Y.; Zhang, X.; Jiao, R. H.; Houk, K. N.; Liang, Y.; Tan, R. X.; Ge, H. M. Nature, 2019, 568, 122–138.

Vibration information in log file




In the log file of freq calculation, there is a place where Frequency is described as follows. Search “Frequencies-“, then you can find it.

Information on the movement of each atom is written below each vibration mode in the x, y, and z directions. As shown below, it is easier to understand to see it with Gauss View’s display.

If you read the vibration value of this part, multiply it by -1.0 to 1.0 and add it to the coordinate information, it will be the coordinate moved in the direction of the imaginary vibration.

Now, let’s explain how to actually save the coordinates moved in the direction of the imaginary vibration!

Option 1. Use Gauss View

If you have Gauss View, select Results > Vibrations. Next, check Manual Displacement, and move the slide bar as shown in the following movie.

If you get the good structure for Reverse and Forward, respectively, click “save structure”.

How to use Gauss View

Option 2. Use the script




Moving coordinates in the direction of an imaginary vibration is a task that can be easily completed with Gauss View, but some people do not have a Gauss View and only have a Gaussian.

For those people, we wrote a simple script that can create the structure moved along with the imaginary vibration! You can download a program written in C ++ from the link below.

In this program, the vibration information is multiplied by -1.0 to 1.0 in increments of 0.1 and added to the optimized coordinates.

Use the following command to execute!

Comparison with the real IRC calculation

We examined the feasibility of this methodology. A comparison of both showed that there was no difference between the one optimized by manually moving in the direction of the imaginary vibration and the one optimized after the IRC calculation.

The trick is to add vibration information at about 0.1 times when changing the structure in the direction of the imaginary vibration.

Adding vibration information at a factor of 1.0 results in a very unnatural structure, and it takes longer to optimize the structure.

To the end, you just need to slip a little from the top of the mountain, TS, and then it will automatically go down the slope.

see also : Transition State? Imaginary Frequency?

Summary

In Computational Details in many papers, authors clearly mention they performed IRC calculations as in the following example.




The intrinsic reaction coordinate (IRC) calculations were performed at the same level of theory to assure the transition states could connect the reactants and expected product.

J Phys Org Chem. 2019, e4035.

Intrinsic reaction coordinate (IRC) calculations were used to characterize transition state structures.

Tetrahedron Lett. 2012, 53, 6919–6922.

As shown above, you “must” carry out IRC calculation after the structure optimization of TS structure!

However, if IRC calculation doesn’t work, why not try moving it slightly in the direction of the imaginary vibration? Of course, you need to clearly mention “IRC calculation did not work” in your paper.

We’ve already introduced an excuse for failing to calculate IRC in our previous article.

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.