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Cyclobutadiene is often described as the //Mona Lisa// of molecules, with an enigmatic smile of its own. After around 100 years of effort, it was finally made. But it has only ever been characterised by NMR and IR spectroscopies. Its structure (bond lengths, shape etc) remains untested by direct experimental observation. One key method remained, x-ray crystallography and in July of 2010, that final missing link was apparently provided by Yves-Marie Legrand, Arie van der Lee and Mihail Barboiu 10.1126/science.1188002. The synthetic scheme used is shown below.
The lactone **1** is first trapped in a calixarene host, and then irradiated (//hv1//) to convert it to the bicyclic isomer, and then with light of different wavenumer (320-500nm, //hv2//) it was induced to fragment to 1,3-dimethylcyclobutadiene and carbon dioxide (or was it?). There these two species remained (at 175K) for long enough for a crystal structure to be determined (duration not stated by the authors, but perhaps ~24 hour?).
Just as the Mona Lisa keeps her secrets, so this synthesis has its own mysteries. Some of these are outlined at this blog. Questions that might be asked (and answered here) include:
1.#1 Can hv2 light be absorbed by molecule **2**? * Would putting **2** inside a calixarene change this absorption? * Would the calixarene absorb so much of hv2 that none would reach **2** inside? * Can energy be transferred from the calixarene to molecule **2**? * If **2** did absorb enough light to induce fragmentation, would this be to molecule **3** or molecules **4**+**5**? * If molecule **3** formed, would it be stable enough to exist long enough for an X-ray determination to be done? * If molecules **4** and **5** formed, would they hang around long enough for an X-Ray. After all, carbon dioxide is a gas! * Would warming the crystals containing putative **4** and **5** result in further reaction? * What interactions might hold all the actors in this play inside the calixarene (i.e. hydrogen bonds?). If such do exist, how do they evolve as the reactions proceed? * Is the particular calixarene design optimal? Could a better be designed? * The original claim was that **4**+**5** hung around long enough for X-ray data to be collected. But might they react together so quickly that X-ray data could not in fact be collected? * Are the structural parameters claimed for **4** and **5** sensible? * For example, the O=C=O angle is claimed as 120 degrees. How much energy does it take to distort carbon dioxide by this amount? Is that distortion energy influenced by surroundings (hydrogen bonds and the like)? * One possible interaction is to X (shown in the scheme). Does such an interaction exist? How strong might it be? * The original report claimed the formation of **4**+**5**, but their data implied the two were particularly intimate. Intimate enough for the C-C distance between them to be 1.5A. This was described as a strong //van der Waals// interaction. Is this reasonable? How strong CAN an vdW interaction be? Is the strength of this interaction influenced by immediate surroundings of the atoms involved (i.e. is there such a thing as a strong vdW interaction, or are they all the same for any given atom pair?) *Or perhaps, if the C-C bond is after all covalent, might the species characterised be instead **3**? * Molecule **2** is presumably formed in enantiomeric pairs. Is the partial occupancy of each of these 50% in the host, or does each cavity contain 100% occupancy of one enantiomer? * The reaction occurs inside a calixarene-based cavity. This includes four guanidinium cations (balancing in charge four sulfonate anions). One of the guanidinium cations is close to the carbon dioxide, and may exert a catalytic effect on the reaction between it and the cyclobutadiene. What happens if it is replaced by another cation? In other words, can the free energy of reaction between **4**+**5** be modified (upwards or downwards) by redesigning the host? * What would happen if the molecule **6** (InChI key JRAGLLKXDATSKP-UHFFFAOYSA-N) were to be used instead? Curiously, this [[http://dx.doi.org/10.1021/ja00837a053|1975 article]] describing the preparation of this molecule, and its extrusion of nitrogen gas, does not seem to have been followed up? * Are there other modifications to **6** which might be more suitable. CS2 for extrusion for example?
One might imagine many more questions to ask. Please put yours here!
-- [[Users/HenryRzepa]]
This page is for information related to the first paper on Quixote for the Journal of Cheminformatics.
The paper is hosted on bitbucket and can be found here:
[[http://bitbucket.org/echeniquep/2011_quixotenewsletter1st_jci]]
The Quixote project has been described at several meetings. This section provides links to the meetings as well as links to the files.
Geoff Hutchison mentioned Quixote in his talk at the Building a Collaborative Framework for Nanoscale Simulations meeting. Geoff's slides can be found here.
The slides prepared by Jens for Geoff, are on the Quxiote Bitbucket site here
Jens presented a poster and some slides about Quixote at the Visions of a Semantic Molecular Future symposium to celebrate the work of Peter Murray-Rust.
The slides and poster are on the Bitbucket site here