Data discoverability

December 17th, 2014

I have written earlier about the Amsterdam Manifesto. That arose out of a conference on the theme of “beyond the PDF“, with one simple question at its heart: what can be done to liberate data from containers it was not designed to be in? The latest meeting on this topic will happen in January 2015 as FORCE2015.

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Cyclopropanation: the mechanism of the Simmons–Smith reaction.

December 14th, 2014

These posts contain the computed potential energy surfaces for a fair few “text-book” reactions. Here I chart the course of the cyclopropanation of alkenes using the Simmons-Smith reagent,[1] as prepared from di-iodomethane using zinc metal insertion into a C-I bond.
simmonds-smith

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References

  1. H.E. Simmons, and R.D. Smith, "A NEW SYNTHESIS OF CYCLOPROPANES FROM OLEFINS", J. Am. Chem. Soc., vol. 80, pp. 5323-5324, 1958. http://dx.doi.org/10.1021/ja01552a080

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

December 7th, 2014

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

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References

  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. http://dx.doi.org/10.1021/ic50038a006

Halogen bonds 3: “Nitrogen tri-iodide”

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.

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Halogen bonds 2: The DABCO-Iodine structure.

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.

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References

  1. Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., "CCDC 879935: Experimental Crystal Structure Determination", 2013. http://dx.doi.org/10.5517/CCYJN03
  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. http://dx.doi.org/10.1021/cg300669t

Halogen bonds: Part 1.

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.

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A computed mechanistic pathway for the formation of an amide from an acid and an amine in non-polar solution.

November 12th, 2014

In London, one has the pleasures of attending occasional one day meetings at the Burlington House, home of the Royal Society of Chemistry. On November 5th this year, there was an excellent meeting on the topic of Challenges in Catalysisand you can see the speakers and (some of) their slides here. One talk on the topic of Direct amide formation – the issues, the art, the industrial application by Dave Jackson caught my interest. He asked whether an amide could be formed directly from a carboxylic acid and an amine without the intervention of an explicit catalyst. The answer involved noting that the carboxylic acid was itself a catalyst in the process, and a full mechanistic exploration of this aspect can be found in an article published in collaboration with Andy Whiting’s group at Durham.[1] My after-thoughts in the pub centered around the recollection that I had written some blog posts about the reaction between hydroxylamine and propanone. Might there be any similarity between the two mechanisms?

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References

  1. H. Charville, D.A. Jackson, G. Hodges, A. Whiting, and M.R. Wilson, "The Uncatalyzed Direct Amide Formation Reaction - Mechanism Studies and the Key Role of Carboxylic Acid H-Bonding", European Journal of Organic Chemistry, vol. 2011, pp. 5981-5990, 2011. http://dx.doi.org/10.1002/ejoc.201100714

The solvation of ion pairs.

November 6th, 2014

Solvolytic mechanisms are amongst the oldest studied, but reproducing their characteristics using computational methods has been a challenging business. This post was inspired by reading Steve Bachrach’s post, itself alluding to this aspect in the title “Computationally handling ion pairs”. It references this recent article on the topic[1] in which the point is made that reproducing the features of both contact and solvent-separated ion pairs needs a model comprising discrete solvent molecules (in this case four dichloromethane units) along with a continuum model.

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References

  1. T. Hosoya, T. Takano, P. Kosma, and T. Rosenau, "Theoretical Foundation for the Presence of Oxacarbenium Ions in Chemical Glycoside Synthesis", J. Org. Chem., vol. 79, pp. 7889-7894, 2014. http://dx.doi.org/10.1021/jo501012s

Blasts from the past. A personal Web presence: 1993-1996.

November 1st, 2014

Egon Willighagen recently gave a presentation at the RSC entitled “The Web – what is the issue” where he laments how little uptake of web technologies as a “channel for communication of scientific knowledge and data” there is in chemistry after twenty years or more. It caused me to ponder what we were doing with the web twenty years ago. Our HTTP server started in August 1993, and to my knowledge very little content there has been deleted (it’s mostly now just hidden). So here are some ancient pages which whilst certainly not examples of how it should be done nowadays, give an interesting historical perspective. In truth, there is not much stuff that is older out there!

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More simple experiments with crystal data. The pyramidalisation of nitrogen.

November 1st, 2014

We are approaching 1 million recorded crystal structures (actually, around 716,000 in the CCDC and just over 300,00 in COD). One delight with having this wealth of information is the simple little explorations that can take just a minute or so to do. This one was sparked by my helping a colleague update a set of interactive lecture demos dealing with stereochemistry. Three of the examples included molecules where chirality originates in stereogenic centres with just three attached groups. An example might be a sulfoxide, for which the priority rule is to assign the lone pair present with atomic number zero. The issue then arises as to whether this centre is configurationally stable, i.e. does it invert in an umbrella motion slowly or quickly.  My initial intention was to see if crystal structures could cast any light at all on this aspect.

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