Posts Tagged ‘free energy’

Molecule-sized pixels.

Sunday, August 11th, 2013

The ultimate reduction in size for an engineer is to a single molecule. It’s been done for a car; now it has been reported for the pixel (picture-element).[1]

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References

  1. J.E. Kwon, S. Park, and S.Y. Park, "Realizing Molecular Pixel System for Full-Color Fluorescence Reproduction: RGB-Emitting Molecular Mixture Free from Energy Transfer Crosstalk", J. Am. Chem. Soc., vol. 135, pp. 11239-11246, 2013. http://dx.doi.org/10.1021/ja404256s

Mechanism of the Boekelheide rearrangement

Wednesday, June 26th, 2013

A reader asked me about the mechanism of the reaction of 2-picoline N-oxide with acetic anhydride to give 2-acetoxymethylpyridine (the Boekelheide Rearrangement[1]). He wrote ” I don’t understand why the system should prefer to go via fragmentation-recombination (… the evidence being that oxygen labelling shows scrambling) when there is an easy concerted pathway available (… a [3,3]sigmatropic shift). Furthermore, is it possible for two pathways to co-exist?” Here is how computation might enlighten us.

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References

  1. A. Massaro, A. Mordini, A. Mingardi, J. Klein, and D. Andreotti, "A New Sequential Intramolecular Cyclization Based on the Boekelheide Rearrangement", European Journal of Organic Chemistry, vol. 2011, pp. 271-279, 2011. http://dx.doi.org/10.1002/ejoc.201000936

Woodward’s symmetry considerations applied to electrocyclic reactions.

Monday, May 20th, 2013

Sometimes the originators of seminal theories in chemistry write a personal and anecdotal account of their work. Niels Bohr[1] was one such and four decades later Robert Woodward wrote “The conservation of orbital symmetry” (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249; it is not online and so no doi can be given). Much interesting chemistry is described there, but (like Bohr in his article), Woodward lists no citations at the end, merely giving attributions by name. Thus the following chemistry (p 236 of this article) is attributed to a Professor Fonken, and goes as follows (excluding the structure in red):

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References

  1. N. Bohr, "Der Bau der Atome und die physikalischen und chemischen Eigenschaften der Elemente", Z. Physik, vol. 9, pp. 1-67, 1922. http://dx.doi.org/10.1007/BF01326955

Au and Pt π-complexes of cyclobutadiene.

Wednesday, May 15th, 2013

In the preceding post, I introduced Dewar’s π-complex theory for alkene-metal compounds, outlining the molecular orbital analysis he presented, in which the filled π-MO of the alkene donates into a Ag+ empty metal orbital and back-donation occurs from a filled metal orbital into the alkene π* MO. Here I play a little “what if” game with this scenario to see what one can learn from doing so.

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Hidden intermediates in the (acid catalysed) ring opening of propene epoxide.

Monday, May 6th, 2013

In a previous post on the topic, I remarked how the regiospecific ethanolysis of propene epoxide[1] could be quickly and simply rationalised by inspecting the localized NBO orbital calculated for either the neutral or the protonated epoxide. This is an application of Hammond’s postulate[[2] in extrapolating the properties of a reactant to its reaction transition state. This approach implies that for acid-catalysed hydrolysis, the fully protonated epoxide is a good model for the subsequent transition state. But is this true? Can this postulate be tested? Here goes.

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References

  1. H.C. Chitwood, and B.T. Freure, "The Reaction of Propylene Oxide with Alcohols", J. Am. Chem. Soc., vol. 68, pp. 680-683, 1946. http://dx.doi.org/10.1021/ja01208a047
  2. G.S. Hammond, "A Correlation of Reaction Rates", J. Am. Chem. Soc., vol. 77, pp. 334-338, 1955. http://dx.doi.org/10.1021/ja01607a027

A sideways look at the mechanism of ester hydrolysis.

Friday, March 29th, 2013

The mechanism of ester hydrolysis is a staple of examination questions in organic chemistry. To get a good grade, one might have to reproduce something like the below. Here, I subject that answer to a reality check.

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Kinetic vs Thermodynamic control. Subversive thoughts for electrophilic substitution of Indole.

Sunday, March 10th, 2013

I mentioned in the last post that one can try to predict the outcome of electrophilic aromatic substitution by approximating the properties of the transition state from those of either the reactant or the (presumed Wheland) intermediate by invoking Hammond’s postulate[1]. A third option is readily available nowadays; calculate the transition state directly. Here are the results of exploring this third variation.

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References

  1. G.S. Hammond, "A Correlation of Reaction Rates", J. Am. Chem. Soc., vol. 77, pp. 334-338, 1955. http://dx.doi.org/10.1021/ja01607a027

The conformation of acetaldehyde: a simple molecule, a complex explanation?

Friday, February 8th, 2013

Consider acetaldehyde (ethanal for progressive nomenclaturists). What conformation does it adopt, and why? This question was posed of me by a student at the end of a recent lecture of mine. Surely, an easy answer to give? Read on …

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Sharpless epoxidation, enantioselectivity and conformational analysis.

Thursday, January 3rd, 2013

I return to this reaction one more time. Trying to explain why it is enantioselective for the epoxide product poses peculiar difficulties. Most of the substituents can adopt one of several conformations, and some exploration of this conformational space is needed.

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How to tame an oxidant: the mysteries of “tpap” (tetra-n-propylammonium perruthenate).

Monday, December 24th, 2012

tpap[1], as it is affectionately known, is a ruthenium-based oxidant of primary alcohols to aldehydes discovered by Griffith and Ley. Whereas ruthenium tetroxide (RuO4) is a voracious oxidant[2], its radical anion countered by a tetra-propylammonium cation is considered a more moderate animal[3]. In this post, I want to try to use quantum mechanically derived energies as a pathfinder for exploring what might be going on (or a reality-check if you like). 

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References

  1. S.V. Ley, J. Norman, W.P. Griffith, and S.P. Marsden, " Tetrapropylammonium Perruthenate, Pr 4 N + RuO 4 - , TPAP: A Catalytic Oxidant for Organic Synthesis ", Synthesis, vol. 1994, pp. 639-666, 1994. http://dx.doi.org/10.1055/s-1994-25538
  2. D.G. Lee, U.A. Spitzer, J. Cleland, and M.E. Olson, "The oxidation of cyclobutanol by ruthenium tetroxide and sodium ruthenate", Canadian Journal of Chemistry, vol. 54, pp. 2124-2126, 1976. http://dx.doi.org/10.1139/v76-304
  3. D.G. Lee, Z. Wang, and W.D. Chandler, "Autocatalysis during the reduction of tetra-n-propylammonium perruthenate by 2-propanol", J. Org. Chem., vol. 57, pp. 3276-3277, 1992. http://dx.doi.org/10.1021/jo00038a009