Tag: deficiency

  • Curly arrow pushing: another reality check.

    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.

  • A short history of molecular modelling: 1860-1890.

    In 1953, the model of the DNA molecule led to what has become regarded as the most famous scientific diagram of the 20th century. It had all started 93 years earlier in 1860, at a time when the tetravalency of carbon was only just established (by William Odling) and the concept of atoms as real entities was to remain controversial for another 45 years (for example Faraday, perhaps the most famous scientist alive in 1860 did not believe atoms were real). So the idea of constructing a molecular model from atoms as the basis for understanding chemical behaviour was perhaps bolder than we might think. It is shown below, part of a set built for August Wilhelm von Hofmann as part of the lectures he delivered at the Royal College of Chemistry in London (now Imperial College).

    The original August Wilhelm von Hofmann molecular model, located in the archives at the Royal institution, London and used by Hofmann in his 1865 lecture there

    This grand-daddy of all molecular models does have some interesting features. The most obvious is that the carbon atom at the centre is square planar (tetrahedral carbon was still 14 years in the future). What HAS survived to the present day is the colour scheme used (black=carbon, white=hydrogen, and not shown here, red=oxygen, blue=nitrogen, green=chlorine).  But another noteworthy aspect is the relative size of the white hydrogen, which is larger than the black carbon. This deficiency was however very soon rectified in 1861 by Josef Loschmidt, who published  a famous pamphlet in which he set out his ideas for the structures of more than  270 molecules (many of which by the way were cyclic, and this some four years before Kekule’s dream!). An example (#239) is shown below, which gets the relative sizes of the atoms more or less correct (OK, chlorine is shown with rather an odd shape). To get an idea of how good Loschmidt’s model actually was, click on the diagram to load a modern model, and compare the two! Even more impressive, these diagrams pre-date van der Waals work on the finite sizes of atoms, first presented in 1873.

    Loschmidt’s molecular models. Click for 3D

    To conclude, I cannot resist showing one more model. Hermann Sachse believed cyclohexane could not be planar. To try to convince people, in 1890 he included a  “flat-packed” model in the pages of a journal article,  evidently believing that people would cut it out, and assemble it into a 3D shape.

    Flat-packed molecular model of cyclohexane

    You might have noticed a theme in the present blog of presenting 3D models for many of the molecules I discuss (include the Loschmidt one above). For the historians amongst you, I note our 1995 article in which we updated[cite]10.1039/P29950000007[/cite] Sachse’s origami with an article featuring how to incorporate interactive models into journals (still sadly only too rare). Perhaps a history of the molecular model, and how it has been presented over 150 years might be an interesting one to trace!


    Acknowledgments

    This post has been cross-posted in PDF format at Authorea.