Archive for the ‘Interesting chemistry’ Category

Halogen bonds 4: The strongest (?) halogen bond.

Sunday, December 7th, 2014

Continuing my hunt, here is a candidate for a strong(est?) halogen bond, this time between Se and I.[1].
The features of interest include:



  1. H. Maddox, and J.D. McCullough, " The Crystal and Molecular Structure of the Iodine Complex of 1-Oxa-4-selenacyclohexane, C 4 H 8 OSe.I 2 ", Inorganic Chemistry, vol. 5, pp. 522-526, 1966.

Halogen bonds 3: “Nitrogen tri-iodide”

Monday, December 1st, 2014

Nitrogen tri-iodide, or more accurately the complex between it and ammonia ranks amongst the oldest known molecules (1812). I became familiar with it around the age of 12-13, in an era long gone when boys (and very possibly girls too) were allowed to make such substances in their parent’s back gardens and in fact in the school science laboratory, an experiment which earned me a personal request to visit the head teacher.


Halogen bonds 2: The DABCO-Iodine structure.

Sunday, November 30th, 2014

Pursuing the topic of halogen bonds, the system DABCO (a tertiary dibase) and iodine form an intriguing complex. Here I explore some unusual features of the structure HEKZOO[1] as published in 2012[2] and ask whether the bonding between the donor (N) and the acceptor (I-I) really is best described as a “non-covalent-interaction” (NCI) or not.



  1. Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., "CCDC 879935: Experimental Crystal Structure Determination", 2013.
  2. A. Peuronen, A. Valkonen, M. Kortelainen, K. Rissanen, and M. Lahtinen, "Halogen Bonding-Based “Catch and Release”: Reversible Solid-State Entrapment of Elemental Iodine with Monoalkylated DABCO Salts", Crystal Growth & Design, vol. 12, pp. 4157-4169, 2012.

Halogen bonds: Part 1.

Saturday, November 29th, 2014

Halogen bonds are less familiar cousins to hydrogen bonds. They are defined as non-covalent interactions (NCI) between a halogen atom (X, acting as a Lewis acid, in accepting electrons) and a Lewis base D donating electrons; D….X-A vs D…H-A. They are superficially surprising, since both D and X look like electron rich species. In fact the electron distribution around X-X (A=X) is highly anisotropic, with the electron rich distribution (the “donor”)  being in a torus encircling the bond, and an electron deficient region (the “acceptor”) lying along the axis of the bond.


WATOC2014 Conference report. Emergent themes.

Thursday, October 9th, 2014

This second report highlights two “themes”, or common ideas that seem to emerge spontaneously from diversely different talks. Most conferences do have them.


WATOC2014 Conference report. Concepts for Organizing Chemical Knowledge

Monday, October 6th, 2014

I am attending a conference. Plenaries at such events can sometimes provide interesting pointers on things to come (and sometimes they simply point to things past). At WATOC2014 in Santiago Chile, the first plenary was by Paul Ayers with the impressive title “Concepts for organising chemical knowledge” which certainly sounds as if it is pointing forward!


Using a polar bond to flip the (stereochemical) outcome of a pericyclic reaction.

Monday, August 4th, 2014

The outcome of pericyclic reactions con depend most simply on three conditions, any two of which determine the third. Whether the catalyst is Δ or hν (heat or light), the topology determining any stereochemistry and the participating electron count (4n+2/4n). It is always neat to conjure up a simple switch to toggle these; heat or light is simple, but what are the options for toggling the electron count? Here is one I have contrived by playing a game with the periodic table. divinylketon The ring closure of a divinylketone is called the Nazarov reaction, it being promoted thermodynamically by coordination of a Lewis acid to atom X. Divinyl ketone can be regarded as a hidden pentadienyl cation, since the C=O bond is polarised Cδ+Oδ- in the time-honoured manner of organic chemistry. In this (formal) resonance form, it becomes part of a pentadienyl cation and can electrocyclise via a 4-electron reaction involving a stereochemical process known as conrotation. The new bond is formed antarafacially (from opposite faces) at the termini of the pentadienyl cation (ωB97XD/6-311G(d,p)/SCRF=dichloromethane.[1]). Note that for the uncatalysed reaction, the barrier is high and the reaction is endothermic but adding a BF3 to the oxygen lowers the barrier and removes the endothermicity.[2] nazarov-Oa nazarov-Oa nazarov-OBF3 So, one can play a game and ask what would happen if the polarity of the C=X bond were to be reversed. This means going left of oxygen in the periodic table, ending at Be.[3] The reaction has a high barrier, but it is strongly exothermic. However the most noteworthy aspect is that the stereochemistry of the electrocyclisation is now disrotatory, with suprafacial bond formation (from the bottom face in the animation below). The stereochemical outcome of this reaction has been flipped by reversing the polarity of the CX bond. nazarov-Beanazarov-Bea This little example shows how a thought game played using the periodic table can then be reality tested by solving appropriate quantum mechanical equations. In this instance, one is not going to rush into the laboratory to try to replicate the experiment, but it might help catalyse new thoughts amongst the readers of this blog.



  1. Henry S. Rzepa., "Gaussian Job Archive for C5H6O", 2014.
  2. Henry S. Rzepa., "Gaussian Job Archive for C5H6BF3O", 2014.
  3. Henry S. Rzepa., "Gaussian Job Archive for C5H6Be", 2014.

Data nightmares: B40 and counting its π-electrons

Saturday, July 19th, 2014

Whilst clusters of carbon atoms are well-known, my eye was caught by a recent article describing the detection of a cluster of boron atoms, B40 to be specific.[1] My interest was in how the σ and π-electrons were partitioned. In a C40, one can reliably predict that each carbon would contribute precisely one π-electron. But boron, being more electropositive, does not always play like that. Having one electron less per atom, one might imagine that a fullerene-like boron cluster would have no π-electrons. But the element has a propensity[2] to promote its σ-electrons into the π-manifold, leaving a σ-hole. So how many π-electrons does B40 have? These sorts of clusters are difficult to build using regular structure editors, and so coordinates are essential. The starting point for a set of coordinates with which to compute a wavefunction was the supporting information. Here is the relevant page: B401 The coordinates are certainly there (that is not always the case), but you have to know a few tricks to make them usable.



  1. H. Zhai, Y. Zhao, W. Li, Q. Chen, H. Bai, H. Hu, Z.A. Piazza, W. Tian, H. Lu, Y. Wu, Y. Mu, G. Wei, Z. Liu, J. Li, S. Li, and L. Wang, "Observation of an all-boron fullerene", Nature Chem, 2014.
  2. H.S. Rzepa, "The distortivity of π-electrons in conjugated boron rings", Phys. Chem. Chem. Phys., vol. 11, pp. 10042, 2009.

Amides and inverting the electronics of the Bürgi–Dunitz trajectory.

Thursday, June 26th, 2014

The Bürgi–Dunitz angle describes the trajectory of an approaching nucleophile towards the carbon atom of a carbonyl group. A colleague recently came to my office to ask about the inverse, that is what angle would an electrophile approach (an amide)? Thus it might approach either syn or anti with respect to the nitrogen, which is a feature not found with nucleophilic attack. amide My first thought was to calculate the wavefunction and identify the location and energy (= electrophilicity) of the lone pairs (the presumed attractor of an electrophile). But a better more direct approach soon dawned. A search of the crystal structure database. Here is the search definition, with the C=O-E angle, the O-E distance and the N-C=O-E torsion defined (also specified for R factor < 5%, no errors and no disorder). search   The first plot is of the torsion vs the distance, for E = H-X (X=O,F, Cl) amides


Kekulé’s vibration: A modern example of its use.

Friday, June 6th, 2014

Following the discussion here of Kekulé’s suggestion of what we now call a vibrational mode (and which in fact now bears his name), I thought I might apply the concept to a recent molecule known as [2.2]paracyclophane. The idea was sparked by Steve Bachrach’s latest post, where the “zero-point” structure of the molecule has recently been clarified as having D2 symmetry.[1]



  1. H. Wolf, D. Leusser, . Mads R. V. Jørgensen, R. Herbst-Irmer, Y. Chen, E. Scheidt, W. Scherer, B.B. Iversen, and D. Stalke, "Phase Transition of [2,2]-Paracyclophane - An End to an Apparently Endless Story", Chemistry - A European Journal, vol. 20, pp. 7048-7053, 2014.