Hello,
I've been working on calculating the concerted reaction mechanism.
I calculated stepwise reactions before, but I never had a chance to work on concerted reactions.
Now, I'm having trouble with pes scan input that how I can write down the keywords about breaking two bonds at the same time.
For example, in stepwise reaction, if I want to break the bonds between atom 1 and 2, I put the keywords just like below.
B 1 2 S 15 0.1
Then, how can I show the bonds breaking between atom 1 and 2, and atom 3 and 4?
What kind of keywords or terms to use?
You can make 2-dimensional scan, and it is safe but very expensive solution
B 1 2 S 15 0.1
B 3 4 S 15 0.1
Will make for you 15*15=225 constrained optimisations. Path is quite specific, lets say you want to san bot from 1.5 to 3.0 it will go like
1.5 1.5
1.6 1.5
1.7 1.5
...
3.0 1.5
3.0 1.6
2.9 1.6
2.8 1.6
...
1.5 1.6
1.5 1.7
1.6 1.7
...
and so on.
normally reaction goes by one of "diagonals" of this square, but be aware that areas around other corners are hard to calculate. For example, if you would try this for SN2 reaction (why would any do so?), with C-X changing from 3 to 1.5 and C-Y from 3.0 to 1.5 - you have chances that calculation will crash around 1.5 1.5 or 3.0 3.0
Keep in mind - number of scans grows quadratically, so scan 1.5-3.0 is twice more expencive than 1.7-2.7
Another solution could be https://gaussian.com/gic/ but I never personally used it.
Finally one can try to make 2 scans independently, running second from critical point of first. That could depend also on calculated mechanism
I think you want to define ghost atoms in the midpoints the bonds and scan the distance between those bonds. Keep the angles fixed and maybe define the distances with the midpoint as a single variable (you need to define a z-matrix)
C-d2-X-d2-C
|
C-d1-X-d1-C
If you're interested, try out to use the PES scan functionality in the Amsterdam Modeling Suite, you can easily set up complicated combined coordinates.
See e.g. here for a Ziegler-Natta polymerization catalyst: https://www.youtube.com/watch?v=tF199cgUdl8&t=122m29s (start around 2h2m)
You can also define multiple scan coordinates, so you can get nD PES scan as well: https://www.scm.com/doc/AMS/Tasks/PES_Scan.html
Hope this helps
As far as I know, since I have been working on reaction mechanisms via enzymes some of the steps automatically get concerted in my reaction pathway (i.e without any unstable intermediate or TS) so my point is if reaction is really a concerted mechanism, your geometry and configuration should automatically tend towards that stable product, try this do your simple scan and optimize final structure and see what you got.
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