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I'm studying a mechanism of aromatic substitution of fluorine which proceeds via an intermediate.

I'm searching for transition state using relaxed surface scan, then I optimize the TS and perform IRC (intrinsic reaction coordinate) calculation to verify the products. The problem is that the intermediate (that I get from IRC) has nearly the same energy as TS (about 1 kcal/mol lower), which doesn't seem right.

I assume that the intermediate geometry is wrong because the IRC makes 2-3 steps towards it and stops, saying the minimum was reached. How can I verify that IRC gives correct results?

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    $\begingroup$ I recommend that you take the result of the IRC calculation and perform a "standard" geometry optimization. Does the energy of the resulting structure match your reactant? Does the TS connect both the reactant and product? Is the barrier you get from your surface scan relatively close to that of the TS search? If that all checks out, then perhaps you just have a very early TS. There's nothing inherently wrong with that. $\endgroup$ – Andrew Rosen Feb 12 at 20:09
  • $\begingroup$ @AndrewRosen I think it's a very flat PES near the TS, I've tried tight IRC (I'm using Gaussian) and it reached minima on both sides with only one step, and obviously energy difference is very small. Actually, I'm comparing different attack sites in my molecule, and some of them has reasonable energy difference between TS and intermediate and other doesn't. I have very little experience in such calculations, so I'm very confused. $\endgroup$ – roma ichenko Feb 13 at 6:17
  • $\begingroup$ I've tried calculating energy at CCSD(T) level of theory, but at that level my intermediate lies higher than both TS, which confuses me even more. Maybe something is fundamentally wrong in my calculations. $\endgroup$ – roma ichenko Feb 13 at 14:30

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