Wednesday, 24 February 2016

A second mechanism for Sn2

The SN2 mechanism is a favourite of first-year undergraduate organic chemistry lectures. It's chunky and easy to understand, but there's a lot of subtlety in there, and it comes up all over the place. It's supposed to be well-understood (as first-year stuff it better be) but a collaboration of physicists at the University of Freiburg and Texas Tech has found another mechanism for it. (Check out the animations in the link - it makes what I'm about to prattle on about a lot clearer.)

What's SN2? Suppose you have a molecule of methyl iodide, CH3-I, but really you want a bromine atom, Br, in there instead of the iodine. Bromine and iodine are both in the same chemical group (the halogens) so it seems like a fair swap. You do this by shoving in some bromide anions (bromine atoms with a negative charge). The iodine that was originally in the molecule comes out as an iodide anion (which is just an iodine atom with a negative charge), balancing things out.

Br- + CH3-I --> Br-CH3 + I-

This process turns the CH3 part of the molecule inside-out, like an umbrella. This mechanism makes a lot of sense, and explains a lot of things seen in experiment - with more complicated molecules, you can see the inverting process happening around that particular carbon atom. And of course there has to be room for the attacking nucleophile to approach - if you stick really big bulky things on that carbon, the nucleophile can't attack, and suddenly the reaction won't go.[1]

Looking at SN2 this way makes it easy to understand what's going on. However it always pays to check your assumptions rigorously, which is how the new mechanism was exposed. The researchers set up an idealised SN2 reaction. They fired a beam of pure Br- into a beam of pure CH3-I molecules, so they know exactly how things are flying together. They monitored what direction and speed the iodide ions were coming out after the swap with in order to figure out what was happening.

In a minority of cases, rather than the bromide whalloping in one side and iodide flying out opposite (as you'd expect from the normal mechanism above), the bromide smacks into the methyl group from an angle. This sends the methyl iodide molecule spinning. The bromide can then snag the methyl part away, leaving an iodide ion. The substrate and products, and even inversion around the attacked carbon are the same (as you can see on the animation on the website).

It's a really neat idea, although the spinning action kind of depends on you having big, heavy atoms to swap in otherwise fairly light little molecules. And the new mechanism only becomes important when the collisions are happening with a lot of energy. It may seem pedantic, but exploring little oddities like this can explain odd behavior.

[1]This kind of reaction is a nucleophilic substitution - the iodide and bromide are nucleophiles (they chase positive charges) and we're swapping one for the other. In this case, if you sit down and monitor how the reaction's speed changes with the concentration of methyl iodide or the amount of bromide, then you see that both matter - this suggests that both the attacking group and the substrate come together in one step to make the reaction go. We say that the process is bimolecular. That's where the odd name comes from - SubsitutionNucleophilic2(Bimolecular).

Original paper. (Science)

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