Posts Tagged ‘intrinsic reaction coordinate’

Curly arrow pushing: another reality check.

Sunday, August 5th, 2012

Two years ago, I discussed how curly arrow pushing is taught, presenting four different ways of showing the arrows. One of the comments posted to that blog suggested that all of the schemes shown below were deficient in one aspect.

Curly arrow pushing

The issues were the stereo and regiochemistry. In particular, the diagram above carries no explicit information about the symmetry of the electrons from which the first arrow originates; it is considered only implicit that we are referring to the π-electrons of the alkene, and that this in turn imparts stereochemical information which is absent from the diagram itself. This deficiency can indeed be traced back to the first ever representation of curly arrows, where the distinction between π- and σ-electrons was not made, and which in that example can cause much confusion about the properties of the molecule being considered. It is in some respects surprising that a notation first proposed in 1924, in effect before quantum mechanics as applied to chemistry had properly matured, is still largely intact and unchanged since that day.

Are curly arrows ripe for reform? In order to try to move this debate forward, I decided to investigate precisely the reaction shown above using quantum mechanics (ωb97xd/6-311g(d,p)/scrf(cpcm=water)  The results will be presented as an intrinsic reaction coordinate of the precise reaction shown above. Before revealing it however, I should note that the scheme above in fact attempts to represent only part of a reaction; the formation of a carbocation by reacting propene with HBr. It does not reveal the end-game so to speak, in which the carbocation then reacts with the bromide anion to form 2-bromopropane. What is implied by the scheme above is that the propyl cation and bromide anion together constitute a discrete intermediate on the way to form this product, and that the overall reaction therefore comprises two discrete transition states and one intermediate; a stepwise reaction.

  1. The (optimised) geometry of the starting point (IRC = 3.5) is a hydrogen bonded complex between the alkene and the H-Br, interacting via the π-cloud of the former. This structure is offset from the mid-point of the double bond towards the less substituted end. We are here seeing Markovnikov’s rule in action.
  2. As a result, the proton transfer (IRC = 0.0) when it starts to happen, heads off for the terminal carbon rather than the middle one.
  3. After this point, note carefully that no intermediate carbocation/bromide anion pair is actually formed. Instead at about IRC -1.0, the bromide atom starts to move towards the central carbon to form a C-Br bond (IRC -2). The immediate outcome of this is that the newly formed C-Br and C-H bonds are conformationally eclipsed.
  4. At IRC -4, the final stage in the reaction starts to take place, a subtle rotation about the BrC-CH bond to remove its eclipsing nature.

If you compare this more quantitative scenario with that depicted in the original scheme at the top, you will notice that it does not capture the timing of any of the events described above and even  appears to be quantitatively wrong in showing a carbocationic intermediate. This last aspect perhaps is because a curly arrow diagram does not attempt to describe the environment in which a reaction might find itself, which in this case may be an explicit hydrogen bonding solvent or Lewis acid catalyst. Thus the bromide anion may be stabilised by other species present in solution, perhaps to the extent of even forming an ion pair.

The point to take home from this however is that perhaps the next evolution of (schematic) curly arrows might be towards more quantitative reaction coordinate diagrams, expressed (as here) as an animated IRC. Indeed, I am (slowly) assembling a library of these for some of the more common reactions to be found in organic chemistry. And we should not forget that even these are defined by the model we construct, which may not include all of the components and conditions actually present when the reactions occur in reality.

Anatomy of a simple reaction: the hydration of an alkene.

Sunday, September 4th, 2011

The hydration of an alkene by an acid is one of those fundamental reactions, taught early on in most chemistry courses. What can quantum mechanics teach us about the mechanism of the reaction?

The hydration of ethene by a hydronium cation.

The diagram below shows us the IRC, or intrinsic reaction coordinate for the process (for definitions, see here), the reaction proceeding from left to right as shown in the scheme above, with a (free energy) barrier of 14.4 kcal/mol and exothermic by a similar amount (wB97XD/6-311G(d,p) with a continuum solvation correction for water).

One first notices that it is not the smooth bell-shaped profile that is normally drawn in text books. It has bumps/detail. What do these mean? Before dissecting, lets look at another plot, this time the RMS (root mean square) gradients of the 3N-6 geometric variables along the reaction coordinates. These reveal two regions where the RMS gradient is almost zero (other than reactant and product).

1 2 3

Hydrogen-bonded reactant

Forming bridged protonated ethene

The transition state Click for 3D.

4 5

Second phase, C-O bond formation

Rotating from eclipsed to staggered

Five distinct stages can be seen.

  1. The hydronium ion approaches the ethene, and forms quite a strong π-facial hydrogen bond.
  2. Water now starts separating from the hydrogen bonded complex, thus relocating the H-bond from the alkene to the water.
  3. The formal transition state (the only one) is reached, with the proton moving from the symmetric bridged ethyl cation to one end, and the water is starting to move to the other end. Not perhaps the most obvious of transition states!
  4. The formation of the C-O bond is now completing, and the C-C bond is now almost purely converted from double to single.
  5. Only at this stage does the eclipsed conformation of the newly formed ethanol start to rotate into a staggered and final conformation.
  6. Overall, the reaction is concerted (if not synchronous), and its reverse would be classified as an E2 elimination.

You can see quite a lot of simple basic principles in chemistry are illustrated along this reaction coordinate. We have space for one more: what happens if you make the alkene very much more reactive? How about cyclobutadiene, which in avoiding anti-aromaticity, has become highly reactive.

Hydration of cyclobutadiene.

The IRC for this variation is shown below. Notice now the much smaller barrier to reaction (~0.4 kcal/mol in ΔG), and the much greater exothermicity overall.

The transition state is also different. It corresponds to proton transfer from the hydronium cation to one carbon of the cyclobutadiene, to form a stabilised allyl cation. In terms of the reverse elimination, this now corresponds to an E1 type, involving an intermediate species, and the reaction is no longer concerted.

The transition state for protonation of cyclobutadiene

I will stop here, reminding that these two simple reactions have taught us a lot about basic organic chemistry.