Previously, I looked at models of how ammonia could be protonated by water to form ammonium hydroxide. The energetic outcome of my model matched the known equilbrium in water as favouring the unprotonated form (pKb ~4.75). I add here two amines for which R=Me3Si and R=CN. The idea is that the first will assist nitrogen protonation by stabilising the positive centre and the second will act in the opposite sense; an exploration if you like of how one might go about computationally designing a non-steric superbasic amine that becomes predominantly protonated when exposed to water (pKb <1)† and is thus more basic than hydroxide anion in this medium.
Posts Tagged ‘energy’
Hypervalency is defined as a molecule that contains one or more main group elements formally bearing more than eight electrons in their valence shell. One example of a molecule so characterised was CLi6 where the description "“carbon can expand its octet of electrons to form this relatively stable molecule“ was used. Yet, in this latter case, the octet expansion is in fact an illusion, as indeed are many examples that are cited. The octet shell remains resolutely un-expanded. Here I will explore the tiny molecule CH3F2- where two extra electrons have been added to fluoromethane.
- H. Kudo, "Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry", Nature, vol. 355, pp. 432-434, 1992. http://dx.doi.org/10.1038/355432a0
The phenomenon of bond stretch isomerism, two isomers of a compound differing predominantly in just one bond length, is one of those chemical concepts that wax and occasionally wane. Here I explore such isomerism for the elements Ge, Sn and Pb.
- J.A. Labinger, "Bond-stretch isomerism: a case study of a quiet controversy", Comptes Rendus Chimie, vol. 5, pp. 235-244, 2002. http://dx.doi.org/10.1016/S1631-0748(02)01380-2
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 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. Here I explore aspects of how the small molecule below might be used to investigate the accuracy of such estimates of dispersion energies.
- 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
- 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
I’ve started so I’ll finish. Mechanism and kinetic isotope effects for protiodecarboxylation of indoles.Saturday, January 2nd, 2016
Another mechanistic study we started in 1972 is here 40+ years on subjected to quantum mechanical scrutiny.
- 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
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.
A tutorial problem in stereoelectronic control. The Tiffeneau-Demjanov rearrangement as part of a prostaglandin synthesis.Monday, November 23rd, 2015
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, the stereochemical outcome being crucial. Here I take a look at this mechanism using computation.
- 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
Yes, no, yes. Computational mechanistic exploration of (nickel-catalysed) cyclopropanation using tetramethylammonium triflate.Thursday, October 1st, 2015
A fascinating re-examination has appeared of a reaction first published in 1960 by Wittig and then 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 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.
- 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
- 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
- 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