Comments on: Secrets of a university tutor: (curly) arrow pushing

By: How is the bromination of alkenes best represented? « Henry Rzepa

How is the bromination of alkenes best represented? « Henry Rzepa — Sun, 14 Oct 2012 20:22:43 +0000

[...] to around 1924, with style that bifurcated into two common types used nowadays (on which I have commented and about which further historical light at the end of this post). Here I try to combine these [...]

By: Henry Rzepa

Henry Rzepa — Fri, 03 Aug 2012 13:57:49 +0000

I now recollect that one of the reaction animations I have included on this blog, and also the library I note above is indeed the simple hydration of an alkene using an acid (H3O+ in fact). The IRC for this does indeed bring out several of the points that Paul makes above, including the H-bonded π-complex, the differences in timing of the arrows, the π-character of the attack. What it does not do is include a methyl substituent on the alkene, to show how in reality the outcome producing a secondary carbocation is favoured over a primary one. This would be easily done, and I shall presently report back on this.

Actually, it does convince me that IRCs may well be a better next step to improve the curly arrow notation we have been using for almost 100 years now.

Postscript: This site by Nick Greeves is called ChemTube3D, and there you can see curly arrows in 3D, rendered using not so much Chemdraw as Jmol. There are kind of a half-way house between the conventional flat curly arrows, and the full QM-IRC.

By: Henry Rzepa

Henry Rzepa — Fri, 03 Aug 2012 13:44:05 +0000

Curly arrow pushing is admittedly very limited. Amongst the aspects it is agnostic about is the three dimensional nature of the system; it is essentially superimposed upon a connection table in 2 dimensions. Some stereochemistry can be added with the usual wedges and hashes, but that in itself is pretty limited. The other aspect that curly arrows do not attempt to capture is the dynamics of the process, the sequence in which things happen. In effect, the assumption is that all the arrows are equal in timing.

I would imagine that any attempt to add these further layers would have to be tempered with regard to the clarity of the outcome, and also the knowledge about the detailed structure of the species. This in turn would require high level calculations, which are not always readily to hand. Curly arrows traditionally required schematic knowledge of a reaction mechanism, not the details.

Certainly, as you may spot on the pages of this blog, I have tried to address some of these aspects by including IRC animations of the reaction.This injects real 3D coordinates (not just 2D connections) and includes (a first order approximation to) the dynamics of the process.

As it happens, I have spent the morning trying to assemble some of these into a reaction library, and this has been mounted on the iTunesU site. It is early days yet with this project, but you are welcome to do the following.

1. Get an iPad.
2. Download the iTunesU app onto it
3. Using this device (and a Browser), click on this link.
4. This will enrol you onto the course (library) and produce thumbnail images of each reaction. Press this and the animation will appear.
5. I am also learning how to produce an iBook of the complete collection as well.

Do please send me comments/suggestion/complaints!

By: Paul Schleyer

Paul Schleyer — Fri, 03 Aug 2012 13:06:38 +0000

Especially for tutorial purposes, all the (a) – (d) alternatives are seriously deficient stereochemically, as they depict a co-planar olefin, and do not bring out the “π-character” of the attack at all. Furthermore, the intermediate BrH-π hydrogen bonded complex is not considered at all. The direction of the curly arrow from this (unsymmetrically bonded) complex shows the orientational prference.

By: The first curly arrows…lead to this? « Henry Rzepa

The first curly arrows…lead to this? « Henry Rzepa — Sat, 21 Jul 2012 13:04:04 +0000

[...] on organic chemistry. Why? It simply breaks the (it has to be said to some extent informal) rules! Consider the dimerisation of nitrosomethane (in fact a well-known [...]

By: The mechanism (in 4D) of the reaction between thionyl chloride and a carboxylic acid. « Henry Rzepa

Fri, 25 May 2012 06:31:45 +0000

[...] I have discussed elsewhere the conventions used in arrow pushing. Nick uses the “American system” , whereas in [...]

By: Shared space (in science). « Henry Rzepa

Shared space (in science). « Henry Rzepa — Fri, 06 Jan 2012 15:48:26 +0000

[...] use metaphors, and how chemists use representations. I have in fact touched upon both of these previously, and it struck me that this last example, of arrow pushing in organic chemistry, was in fact a nice [...]

By: David Denver Deals

David Denver Deals — Tue, 22 Nov 2011 00:45:31 +0000

I find it harder to understand using the arrow pushing. I think a software that does this would help out a lot. Thanks for posting this controversial article on tutoring

By: Angelina S. Tompkins

Angelina S. Tompkins — Sun, 25 Sep 2011 01:42:39 +0000

Is chemdraw a software of just a method to use for making the curves ?

By: Kathlene M. Riles

Kathlene M. Riles — Sun, 25 Sep 2011 01:36:29 +0000

I am looking for some textbooks that explains the breakdowns of each formulas because some reactions are base on the wrong mixture of chemicals.

By: Computational “reality checks” for mechanistic speculations. « Henry Rzepa

Thu, 01 Sep 2011 13:42:49 +0000

[...] a very common indulgence in almost all articles reporting such, and largely based on informed arrow pushing. This process is bound to follow the rules of reasonable Lewis structures for any putative [...]

By: Lacy Campbell

Lacy Campbell — Tue, 23 Aug 2011 05:37:47 +0000

I was taught the same as Bogdan and I always use check-sum rules!

Lacy C.
My Website/Blog – Wooden Garage Doors

By: Bogdan Marekha

Bogdan Marekha — Thu, 19 May 2011 22:30:46 +0000

When I was taught the electrophilic addition to alkenes, the mechanism for hydrohalogens was explained in the context of stereochemical and kinetic results – the prevalence of the anti-product and the second order with respect to HX for trivial substrates – thus assuming a trimolecular (or a two-step bimolecular) reaction with a 3-membered cyclic protonated intermediate rather than a discrete carbocation.

As for the curvy arrows as a tool for drawing “electronic dance” to describe a mechanism on a paper, from my personal experience I believe a tutor has to make students keep in mind that a solid stick represents a 2-electron bond and that the number of valence eletrons (or the net charge of a system) is conserved. This should prevent a number of weird mechanisms.

However, a general chemical thinking has to be the driving force in deriving the “choreo” pattern rather than just attempts to rearrange sticks, dots, arrows, etc. And your blog is a fascinating example on the web of the power of computational chemistry to prove or to question some idea that is used throughout to explain some fenomena.

As my organic chemistry lecturer said “paper will tolerate it all, Nature doesn’t care for it”

By: The oldest reaction mechanism: updated! « Henry Rzepa

The oldest reaction mechanism: updated! « Henry Rzepa — Tue, 02 Nov 2010 07:59:18 +0000

[...] phenomenon, coincident more or less with the development of electronic theories of chemistry. Hence electronic arrow pushing as a term. But here I argue that the true origin of this immensely powerful technique in chemistry [...]