Henry Rzepa's Blog Chemistry with a twist

February 27, 2015

How many water molecules does it take to ionise HF and HBr?

Filed under: General,Interesting chemistry — Tags: , — Henry Rzepa @ 7:43 pm

No doubt answers to the question posed in the previous post are already being obtained by experiment. Just in case that does not emerge in the next day or so, I offer a prediction here.


October 2, 2013

A short non-bonding H…H interaction (continued)

Filed under: Interesting chemistry — Tags: , , — Henry Rzepa @ 9:36 pm

This is a continuation of the discussion started on Steve Bachrach’s blog about a molecule with a very short H…H interaction involving two Si-H groups with enforced proximity. It had been inferred from the X-ray structure[1] that the H…H distance was in the region of 1.50Å. It’s that cis-butene all over again! So is that H…H region a bond? Is it attractive or repulsive? Go read Steve’s blog first.



  1. J. Zong, J.T. Mague, and R.A. Pascal, "Exceptional Steric Congestion in an in,in-Bis(hydrosilane)", Journal of the American Chemical Society, vol. 135, pp. 13235-13237, 2013. http://dx.doi.org/10.1021/ja407398w

October 17, 2012

Trimethylenemethane Ruthenium benzene

Filed under: Interesting chemistry — Tags: , , — Henry Rzepa @ 4:59 pm

Every once in a while, one encounters a molecule which instantly makes an interesting point. Thus Ruthenium is ten electrons short of completing an 18-electron shell, and it can form a complex with benzene on one face and a ligand known as trimethylenemethane on the other[1].



  1. G.E. Herberich, and T.P. Spaniol, "Trimethylenemethane complexes of ruthenium via the trimethylenemethane dianion", Journal of the Chemical Society, Chemical Communications, pp. 1457, 1991. http://dx.doi.org/10.1039/C39910001457

September 15, 2012

Frozen Semibullvalene: a holy grail (and a bis-homoaromatic molecule).

Semibullvalene is an unsettling molecule. Whilst it has a classical structure describable by a combination of Lewis-style two electron and four electron bonds, its NMR behaviour reveals it to be highly fluxional. This means that even at low temperatures, the position of these two-electron bonds rapidly shifts in the equilibrium shown below. Nevertheless, this dynamic behaviour can be frozen out at sufficiently low temperatures. But the barrier was sufficiently low that a challenge was set; could one achieve a system in which the barrier was removed entirely, to freeze out the coordinates of the molecule into a structure where the transition state (shown at the top) became instead a true minimum (bottom)? A similar challenge had been set for freezing out the transition state for the Sn2 reaction into a minimum, the topic also of a more recent post here. Here I explore how close we might be to achieving inversion of the semibullvalene [3,3] sigmatropic potential.


July 29, 2012

Cyclopentadiene: a hydrocarbon at the crossroads of …

Filed under: Uncategorised — Tags: , , , , , — Henry Rzepa @ 3:43 pm

organic chemistry. It does not look like much, but this small little molecule brought us ferrocene, fluxional NMR, aromatic anions and valley-ridge inflexion points. You might not have heard of this last one, but in fact I mentioned the phenomenon in my post on nitrosobenzene. As for being at a crossroads, more like a Y-junction. Let me explain why.


May 18, 2011

The inner secrets of the DNA structure.

In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets.


December 30, 2010

The melting points from benzene to cyclohexane: a prime example of dispersion forces in action?

Filed under: Uncategorised — Tags: , , , , , , — Henry Rzepa @ 11:02 am

One of the delights of wandering around an undergraduate chemistry laboratory is discussing the unexpected, if not the outright impossible, with students. The >100% yield in a reaction is an example. This is sometimes encountered (albeit only briefly) when students attempt to recrystallise a product from cyclohexane, and get an abundant crop of crystals when they put their solution into an ice-bath to induce the crystallisation. Of the solvent of course! I should imagine 1000% yields are possible like this.


November 20, 2010

Data-round-tripping: moving chemical data around.

For those of us who were around in 1985, an important chemical IT innovation occurred. We could acquire a computer which could be used to draw chemical structures in one application, and via a mysterious and mostly invisible entity called the clipboard, paste it into a word processor (it was called a Macintosh). Perchance even print the result on a laserprinter. Most students of the present age have no idea what we used to do before this innovation! Perhaps not in 1985, but at some stage shortly thereafter, and in effect without most people noticing, the return journey also started working, the so-called round trip. It seemed natural that a chemical structure diagram subjected to this treatment could still be chemically edited, and that it could make the round trip repeatedly. Little did we realise how fragile this round trip might be. Years later, the computer and its clipboard, the chemistry software, and the word processor had all moved on many generations (it is important to flag that three different vendors were involved, all using proprietary formats to weave their magic). And (on a Mac at least) the round-tripping no longer worked. Upon its return to (Chemdraw in this instance), it had been rendered inert, un-editable, and devoid of semantic meaning unless a human intervened. By the way, this process of data-loss is easily demonstrated even on this blog. The chemical diagrams you see here are similarly devoid of data, being merely bit-mapped JPG images. Which is why, on many of these posts, I put in the caption Click for 3D, which gives you access to the chemical data proper (in CML or other formats). And I throw in a digital repository identifier for good measure should you want a full dataset.


Powered by WordPress