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I am trying to understand the interaction between the nucleophile and the substrate for some SN2 reactions (e.g. $\ce{I- +CH3Cl->CH3I + Cl-}$) at the transition states. Now, it seems that EDA would be able to analyse this interaction.

But the problem is that the program I am using (GAMESS) requires the charge and multiplicity of each of the fragments to be defined. I have done EDA before with neutral systems. In this case, I am not sure how to define the charges at the transition state, because from what I know, at transition state, the negative charge is delocalised, mainly between the nucleophile and the leaving group (so each of them can be assumed to have, roughly +1/2 charge). I have no idea how to set the multiplicity either, but I guess leaving all to 1 could work. The way the program calculates EDA is by calculating each fragment separately, and then the supermolecule, so there is no way to avoid setting charges and multiplicities.

I have also found multiple papers online which have used EDA on transition states (e.g. this), so it is definitely doable.

Can anyone help me with this?

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    $\begingroup$ +1. Thanks for the bounty. We are a new site and might not have people to answer. If you post on twitter and tag @StackMatter we can re-tweet for you. Also if you tag the authors of people you think might know the answer, it will help. It worked for this question: mattermodeling.stackexchange.com/q/1926/5. As you see that the main developer of the software answered, and then someone also got their grad student to answer, both of them were not users of this site before, and both of them interacted with this tweet: twitter.com/StackMatter/status/1291159713636405249. $\endgroup$ Nov 9 '20 at 21:03
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Very interesting question. I have no experience doing EDA, but as I'll probably need to do it in the future, I used your question as a starting point to learn more about it. I did some research, but unfortunately could not find clear guidance on how to set the charges. In the Gamess (US) user group, a user called Marcela Tormena posted a small but detailed tutorial on how to do EDA on a transition state. But her example system involved only neutral species, so there was no advice on charge assignment.

I also found a article[1] suggesting a split in 3 fragments, with both attacking and leaving groups charged -1, and the central part charged +1, adding to a net charge of -1:

Thirdly, the particular choice of molecular fragments for the EDA needs attention, because the absolute values of each of the energy terms will depend intimately on this.Here we consider that the correspondence between the energies and properties of the TS as well as the reactant and product states of the SN2 reaction Y(-) + RX --> X(-)- + RY can best be characterised from the fully separated fragments X(-) + R(+) + Y(-).[21] Our choice of fragments differs from that used by Bickelhaupt and co-workers, who decomposed the energy of interaction of X- and RY. In addition to comparing all energies to common origin, our approach has the ad-vantage of eliminating the use of activation strain analysisas introduced by Bickelhaupt.[32]Moreover, we think that it is more realistic to consider the nascent and the breaking bonds simultaneously because they are closely associated with each other. This holds in particular for the transition structure in which the two bonds are equally important.

Note in his systems, both nucleophile and leaving group are the same, while in yours these are different species, so I don't know if the same consideration applies.

While not a definitive answer, I hope this is helpful.

References:

  1. Fernández, Israel, et al. “The Interplay between Steric and Electronic Effects in SN2 Reactions.” Chemistry – A European Journal, vol. 15, no. 9, 2009, pp. 2166–75. Wiley Online Library, doi:https://doi.org/10.1002/chem.200801833.
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    $\begingroup$ Thank you very much! This solved most of the problems I was having. I will try the method in the paper you mentioned, hopefully that should give some meaningful results. $\endgroup$
    – S R Maiti
    Nov 12 '20 at 22:07

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