Posts Tagged ‘energy’

A molecular balance for dispersion energy?

Sunday, February 7th, 2016
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The geometry of cyclo-octatetraenes differs fundamentally from the lower homologue benzene in exhibiting slow (nuclear) valence bond isomerism rather than rapid (electronic) bond-equalising resonance. In 1992 Anderson and Kirsch[1] exploited this property to describe a simple molecular balance for estimating how two alkyl substituents on the ring might interact via the (currently very topical) mechanism of dispersion (induced-dipole-induced-dipole) attractions. These electron correlation effects are exceptionally difficult to model using formal quantum mechanics and are nowadays normally replaced by more empirical functions such as Grimme's D3BJ correction.[2] Here I explore aspects of how the small molecule below might be used to investigate the accuracy of such estimates of dispersion energies.

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References

  1. J.E. Anderson, and P.A. Kirsch, "Structural equilibria determined by attractive steric interactions. 1,6-Dialkylcyclooctatetraenes and their bond-shift and ring inversion investigated by dynamic NMR spectroscopy and molecular mechanics calculations", J. Chem. Soc., Perkin Trans. 2, pp. 1951, 1992. http://dx.doi.org/10.1039/P29920001951
  2. S. Grimme, S. Ehrlich, and L. Goerigk, "Effect of the damping function in dispersion corrected density functional theory", J. Comput. Chem., vol. 32, pp. 1456-1465, 2011. http://dx.doi.org/10.1002/jcc.21759

Quintuple bonds: resurfaced.

Sunday, January 31st, 2016
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Six years ago, I posted on the nature of a then recently reported[1] Cr-Cr quintuple bond. The topic resurfaced as part of the discussion on a more recent post on NSF3, and a sub-topic on the nature of the higher order bonding in C2. The comment made a connection between that discussion and the Cr-Cr bond alluded to above. I responded briefly to that comment, but because I want to include 3D rotatable surfaces, I expand the discussion here and not in the comment.

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References

  1. C. Hsu, J.K. Yu, C. Yen, G. Lee, Y. Wang, and Y. Tsai, "Quintuply-Bonded Dichromium(I) Complexes Featuring Metal-Metal Bond Lengths of 1.74 Å", Angewandte Chemie International Edition, vol. 47, pp. 9933-9936, 2008. http://dx.doi.org/10.1002/anie.200803859

I’ve started so I’ll finish. Mechanism and kinetic isotope effects for protiodecarboxylation of indoles.

Saturday, January 2nd, 2016
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Another mechanistic study we started in 1972[1] is here 40+ years on subjected to quantum mechanical scrutiny.

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References

  1. B.C. Challis, and H.S. Rzepa, "Heteroaromatic hydrogen exchange reactions. Part 9. Acid catalysed decarboxylation of indole-3-carboxylic acids", J. Chem. Soc., Perkin Trans. 2, pp. 281, 1977. http://dx.doi.org/10.1039/P29770000281

A tutorial problem in stereoelectronic control. A Grob alternative to the Tiffeneau-Demjanov rearrangement?

Saturday, November 28th, 2015
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In answering tutorial problems, students often need skills in deciding how much time to spend on explaining what does not happen, as well as what does. Here I explore alternatives to the mechanism outlined in the previous post to see what computation has to say about what does (or might) not happen.

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A tutorial problem in stereoelectronic control. The Tiffeneau-Demjanov rearrangement as part of a prostaglandin synthesis.

Monday, November 23rd, 2015
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This reaction emerged a few years ago (thanks Alan!) as a tutorial problem in organic chemistry, in which students had to devise a mechanism for the reaction and use this to predict the stereochemical outcome at the two chiral centres indicated with *.  It originates in a brief report from R. B. Woodward’s group in 1973 describing a prostaglandin synthesis,[1] the stereochemical outcome being crucial. Here I take a look at this mechanism using computation.

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References

  1. R.B. Woodward, J. Gosteli, I. Ernest, R.J. Friary, G. Nestler, H. Raman, R. Sitrin, C. Suter, and J.K. Whitesell, "Novel synthesis of prostaglandin F2.alpha.", J. Am. Chem. Soc., vol. 95, pp. 6853-6855, 1973. http://dx.doi.org/10.1021/ja00801a066

The roles of water in the hydrolysis of an acetal.

Wednesday, November 18th, 2015
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In the previous post, I pondered how a substituent (X below) might act to slow down the hydrolysis of an acetal. Here I extend that by probing the role of water molecules in the mechanism of acetal hydrolysis.

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Yes, no, yes. Computational mechanistic exploration of (nickel-catalysed) cyclopropanation using tetramethylammonium triflate.

Thursday, October 1st, 2015
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A fascinating re-examination has appeared[1] of a reaction first published[2] in 1960 by Wittig and then[3] repudiated by him in 1964 since it could not be replicated by a later student. According to the new work, the secret to a successful replication seems to be the presence of traces of a nickel catalyst (originally coming from e.g. a nickel spatula?). In this recent article[1] a mechanism for the catalytic cycle is proposed. Here I thought I might explore this mechanism using calculations to see if any further insights might emerge.

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References

  1. S.A. Künzi, J.M. Sarria Toro, T. den Hartog, and P. Chen, " Nickel-Catalyzed Cyclopropanation with NMe 4 OTf and n BuLi ", Angewandte Chemie International Edition, vol. 54, pp. 10670-10674, 2015. http://dx.doi.org/10.1002/anie.201505482
  2. V. Franzen, and G. Wittig, "Trimethylammonium-methylid als Methylen-Donator", Angewandte Chemie, vol. 72, pp. 417-417, 1960. http://dx.doi.org/10.1002/ange.19600721210
  3. G. Wittig, and D. Krauss, "Cyclopropanierungen bei Einwirkung vonN-Yliden auf Olefine", Justus Liebigs Ann. Chem., vol. 679, pp. 34-41, 1964. http://dx.doi.org/10.1002/jlac.19646790106

Natural abundance kinetic isotope effects: mechanism of the Baeyer-Villiger reaction.

Wednesday, June 10th, 2015
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I have blogged before about the mechanism of this classical oxidation reaction. Here I further explore computed models, and whether they match the observed kinetic isotope effects (KIE) obtained using the natural-abundance method described in the previous post.

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The mechanism of borohydride reductions. Part 1: ethanal.

Sunday, April 12th, 2015
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Sodium borohydride is the tamer cousin of lithium aluminium hydride (LAH). It is used in aqueous solution to e.g. reduce aldehydes and ketones, but it leaves acids, amides and esters alone. Here I start an exploration of why it is such a different reducing agent.
BH4

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A better model for the mechanism of Lithal (LAH) reduction of cinnamaldehyde?

Friday, April 10th, 2015
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Previously on this blog: modelling the reduction of cinnamaldehyde using one molecule of lithal shows easy reduction of the carbonyl but a high barrier at the next stage, the reduction of the double bond. Here is a quantum energetic exploration of what might happen when a second LAH is added to the brew (the usual ωB97XD/6-311+G(d,p)/SCRF=diethyl ether).

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