Posts Tagged ‘animation’
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. 
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] 
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.‡ 
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.
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References
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Henry S. Rzepa., "Gaussian Job Archive for C5H6O", 2014. http://dx.doi.org/10.6084/m9.figshare.1125721
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Henry S. Rzepa., "Gaussian Job Archive for C5H6BF3O", 2014. http://dx.doi.org/10.6084/m9.figshare.1125724
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Henry S. Rzepa., "Gaussian Job Archive for C5H6Be", 2014. http://dx.doi.org/10.6084/m9.figshare.1125792
Tags:animation, Interesting chemistry, pericyclic
Posted in Uncategorised | No Comments »
Wednesday, March 12th, 2014
My previous post related to the aromatic electrophilic substitution of benzene using as electrophile phenyl diazonium chloride. Another prototypical reaction, and again one where benzene is too inactive for the reaction to occur easily, is the catalyst-free bromination of benzene to give bromobenzene and HBr.
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Tags:activation energy, animation, aromatic, Boris Galabov, co-author, electrophilic, Interesting chemistry, lowest energy solution, o/p director of aromatic electrophilic substitution, Paul Schleyer, pence, substitution
Posted in reaction mechanism | 7 Comments »
Saturday, November 23rd, 2013
Mercury (IV) tetrafluoride attracted much interest when it was reported in 2007[1] as the first instance of the metal being induced to act as a proper transition element (utilising d-electrons for bonding) rather than a post-transition main group metal (utilising just s-electrons) for which the HgF2 dihalide would be more normal (“Is mercury now a transition element?”[2]). Perhaps this is the modern equivalent of transmutation! Well, now we have new speculation about how to induce the same sort of behaviour for caesium; might it form CsF3 (at high pressures) rather than the CsF we would be more familiar with.[3] Here I report some further calculations inspired by this report.
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References
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X. Wang, L. Andrews, S. Riedel, and M. Kaupp, "Mercury Is a Transition Metal: The First Experimental Evidence for HgF4", Angewandte Chemie International Edition, vol. 46, pp. 8371-8375, 2007. http://dx.doi.org/10.1002/anie.200703710
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M. Miao, "Caesium in high oxidation states and as a p-block element", Nature Chemistry, vol. 5, pp. 846-852, 2013. http://dx.doi.org/10.1038/nchem.1754
Tags:animation, energy, free energy barrier, free energy change, Hypervalency, Interesting chemistry, metal, pence, post-transition main group metal, potential energy surface
Posted in Uncategorised | 13 Comments »
Sunday, December 9th, 2012
Sharpless epoxidation converts a prochiral allylic alcohol into the corresponding chiral epoxide with > 90% enantiomeric excess[1],[2]. Here is the first step in trying to explain how this magic is achieved.
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References
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J.M. Klunder, S.Y. Ko, and K.B. Sharpless, "Asymmetric epoxidation of allyl alcohol: efficient routes to homochiral .beta.-adrenergic blocking agents", The Journal of Organic Chemistry, vol. 51, pp. 3710-3712, 1986. http://dx.doi.org/10.1021/jo00369a032
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R.M. Hanson, and K.B. Sharpless, "Procedure for the catalytic asymmetric epoxidation of allylic alcohols in the presence of molecular sieves", The Journal of Organic Chemistry, vol. 51, pp. 1922-1925, 1986. http://dx.doi.org/10.1021/jo00360a058
Tags:animation, asymmetric epoxidation, catalysis, Enantioselective, free energy, Interesting chemistry, lower energy conformations, Reaction Mechanism, Tutorial material
Posted in Uncategorised | 1 Comment »
Wednesday, December 14th, 2011
In this earlier post, I described how the stereochemistry of π2+π2 cycloadditions occurs suprafacially if induced by light, and how one antarafacial component appears if the reaction is induced by heat alone. I also noted how Woodward and Hoffmann (WH) explained that violations to their rules were avoided by mandating a change in mechanism requiring stepwise pathways with intermediates along the route. Here I illustrate how the stereochemistry of a thermal π2+π2 cycloaddition can indeed avoid an antarafacial component by performing appropriate gymnastic contortions instead of a mechanistic change (a WH violation certainly in the letter of their law, if not their spirit).
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Tags:animation, Interesting chemistry, pericyclic, Tutorial material
Posted in Uncategorised | 4 Comments »
Friday, November 25th, 2011
In the previous post, I wrote about the processes that might be involved in a molecular wheel rotating. A nano car has four wheels, and surely the most amazing thing is how the wheels manage to move in synchrony. This is one hell of a tough problem, and I do not attempt an answer here, but simply record an odd observation.
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Tags:animation, Interesting chemistry, nano car
Posted in Uncategorised | 2 Comments »
Tuesday, November 1st, 2011
My previous post introduced the interesting guts of taxol. Two different isomers can exist, and these are called atropisomers; one has the carbonyl group pointing up, the other down. The barrier to their interconversion in this case is generated by a rotation about the two single bonds connecting the carbonyl group to the rest of the molecule. Introductory chemistry tells us that the barrier for rotation about such single bonds is low (i.e. fast at room temperature). But is that true here?
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Tags:animation, conformational analysis, Interesting chemistry, Taxol, Tutorial material
Posted in Uncategorised | 4 Comments »
Sunday, October 16th, 2011
I asked a while back whether blogs could be considered a serious form of scholarly scientific communication (and so has Peter Murray-Rust more recently). A case for doing so might be my post of about a year ago, addressing why borane reduces a carboxylic acid, but not its ester, where I suggested a possible mechanism. Well, colleagues have raised some interesting questions, both on the blog itself and more silently by email to me. As a result, I have tried to address some of these questions, and accordingly my original scheme needs some revision! This sort of iterative process of getting to the truth with the help of the community (a kind of crowd-sourced chemistry) is where I feel blogs do have a genuine role to play.
The reduction of a carboxylic acid by borane
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Tags:activation energy, animation, carboxylic acid, carboxylic ester, diborane, free energy, Interesting chemistry, pericyclic, Peter Murray-Rust, Reaction Mechanism, reduction, Tutorial material
Posted in Uncategorised | 8 Comments »
Saturday, June 11th, 2011
In a time when large (molecules) are considered beautiful (or the corollary that beauty must be big), it is good to reflect that small molecules may teach us something as well. Take ethane. Is there anything left which has not been said about it already? Well, consider the reaction below, in which two hydrogen atoms mutually hop from one carbon to the other.
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Tags:animation, antiaromaticity, cyclic electron systems, distorsion, dyotropic, pericyclic, Tutorial material
Posted in Uncategorised | 4 Comments »
