Henry Rzepa's Blog Chemistry with a twist

April 25, 2019

Imaging normal vibrational modes of a single molecule of CoTPP: a mystery about the nature of the imaged species.

Previously, I explored (computationally) the normal vibrational modes of Co(II)-tetraphenylporphyrin (CoTPP) as a “flattened” species on copper or gold surfaces for comparison with those recently imaged[1]. The initial intent was to estimate the “flattening” energy. There are six electronic possibilities for this molecule on a metal surface. Respectively positively, or negatively charged and a neutral species, each in either a low or a high-spin electronic state. I reported five of these earlier, finding each had quite high barriers for “flattening” the molecule. For the final 6th possibility, the triplet anion, the SCF (self-consistent-field) had failed to converge, but for which I can now report converged results.



  1. J. Lee, K.T. Crampton, N. Tallarida, and V.A. Apkarian, "Visualizing vibrational normal modes of a single molecule with atomically confined light", Nature, vol. 568, pp. 78-82, 2019. http://dx.doi.org/10.1038/s41586-019-1059-9

April 4, 2019

Smoke and mirrors. All is not what it seems with this Sn2 reaction!

Previously, I explored the Graham reaction to form a diazirine. The second phase of the reaction involved an Sn2′ displacement of N-Cl forming C-Cl. Here I ask how facile the simpler displacement of C-Cl by another chlorine might be and whether the mechanism is Sn2 or the alternative Sn1. The reason for posing this question is that as an Sn1 reaction, simply ionizing off the chlorine to form a diazacyclopropenium cation might be a very easy process. Why? Because the resulting cation is analogous to the cyclopropenium cation, famously proposed by Breslow as the first example of a 4n+2 aromatic ring for which the value of n is zero and not 1 as for benzene.[1] Another example of a famous “Sn1” reaction is the solvolysis of t-butyl chloride to form the very stable tertiary carbocation and chloride anion (except in fact that it is not an Sn1 reaction but an Sn2 one!)



  1. R. Breslow, "SYNTHESIS OF THE s-TRIPHENYLCYCLOPROPENYL CATION", Journal of the American Chemical Society, vol. 79, pp. 5318-5318, 1957. http://dx.doi.org/10.1021/ja01576a067

February 18, 2019

The Graham reaction: Deciding upon a reasonable mechanism and curly arrow representation.

Students learning organic chemistry are often asked in examinations and tutorials to devise the mechanisms (as represented by curly arrows) for the core corpus of important reactions, with the purpose of learning skills that allow them to go on to improvise mechanisms for new reactions. A common question asked by students is how should such mechanisms be presented in an exam in order to gain full credit? Alternatively, is there a single correct mechanism for any given reaction? To which the lecturer or tutor will often respond that any reasonable mechanism will receive such credit. The implication is that a mechanism is “reasonable” if it “follows the rules”. The rules are rarely declared fully, but seem to be part of the absorbed but often mysterious skill acquired in learning the subject. These rules also include those governing how the curly arrows should be drawn. Here I explore this topic using the Graham reaction.[1]



  1. W.H. Graham, "The Halogenation of Amidines. I. Synthesis of 3-Halo- and Other Negatively Substituted Diazirines1", Journal of the American Chemical Society, vol. 87, pp. 4396-4397, 1965. http://dx.doi.org/10.1021/ja00947a040

February 24, 2018

Hypervalent or not? A fluxional triselenide.

Another post inspired by a comment on an earlier one; I had been discussing compounds of the type I.In (n=4,6) as possible candidates for hypervalency. The comment suggests the below as a similar analogue, deriving from observations made in 1989.[1]



  1. Y. Mazaki, and K. Kobayashi, "Structure and intramolecular dynamics of bis(diisobutylselenocarbamoyl) triselenide as identified in solution by the 77Se-NMR spectroscopy", Tetrahedron Letters, vol. 30, pp. 2813-2816, 1989. http://dx.doi.org/10.1016/S0040-4039(00)99132-9

November 28, 2017

Octet expansion and hypervalence in dimethylidyne-λ6-sulfane.

Filed under: Historical,Hypervalency — Tags: , , , , , , , — Henry Rzepa @ 9:25 pm

I started this story by looking at octet expansion and hypervalence in non-polar hypercoordinate species such as S(-CH3)6, then moved on to S(=CH2)3. Finally now its the turn of S(≡CH)2.


September 16, 2017

The di-anion of dilithium (not the Star Trek variety): Another “Hyper-bond”?

Early in 2011, I wrote about how the diatomic molecule Be2 might be persuaded to improve upon its normal unbound state (bond order ~zero) by a double electronic excitation to a strongly bound species. I yesterday updated this post with further suggestions and one of these inspired this follow-up.


April 6, 2017

The conformation of enols: revealed and explained.

Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.


March 2, 2017

More tetrahedral fun. Spherical aromaticity (and other oddities) in N4 and C4 systems?

The thread thus far. The post about Na2He introduced the electride anionic counter-ion to Na+ as corresponding topologically to a rare feature known as a non-nuclear attractor. This prompted speculation about other systems with such a feature, and the focus shifted to a tetrahedral arrangement of four hydrogen atoms as a dication, sharing a total of two valence electrons. The story now continues here.


January 2, 2017

Ritonavir: a look at a famous example of conformational polymorphism.

Here is an inside peek at another one of Derek Lowe’s 250 milestones in chemistry, the polymorphism of Ritonavir.[1] The story in a nutshell concerns one of a pharma company’s worst nightmares; a drug which has been successfully brought to market unexpectedly “changes” after a few years on market to a less effective form (or to use the drug term, formulation). This can happen via a phenomenon known as polymorphism, where the crystalline structure of a molecule can have more than one form.[2],[3] In this case, form I was formulated into soluble tablets for oral intake. During later manufacturing, a new less-soluble form appeared and “within weeks this new polymorph began to appear throughout both the bulk drug and formulation areas[1]



  1. J. Bauer, S. Spanton, R. Henry, J. Quick, W. Dziki, W. Porter, and J. Morris, "Array", Pharmaceutical Research, vol. 18, pp. 859-866, 2001. http://dx.doi.org/10.1023/A:1011052932607
  2. J.D. Dunitz, and J. Bernstein, "Disappearing Polymorphs", Accounts of Chemical Research, vol. 28, pp. 193-200, 1995. http://dx.doi.org/10.1021/ar00052a005
  3. D. Bučar, R.W. Lancaster, and J. Bernstein, "Disappearing Polymorphs Revisited", Angewandte Chemie International Edition, vol. 54, pp. 6972-6993, 2015. http://dx.doi.org/10.1002/anie.201410356

September 11, 2016

What’s in a name? Carbenes: a reality check.

To quote from Wikipedia: in chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The most ubiquitous type of carbene of recent times is the one shown below as 1, often referred to as a resonance stabilised or persistent carbene. This type is of interest because of its ability to act as a ligand to an astonishingly wide variety of metals, with many of the resulting complexes being important catalysts. The Wiki page on persistent carbenes shows them throughout in form 1 below, thus reinforcing the belief that they have a valence of two and by implication six (2×2 shared + 2 unshared) electrons in the valence shell of carbon. Here I consider whether this name is really appropriate.


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