Posts Tagged ‘energy’

Molecule orbitals as indicators of reactivity: bromoallene.

Thursday, September 1st, 2016
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Bromoallene is a pretty simple molecule, with two non-equivalent double bonds. How might it react with an electrophile, say dimethyldioxirane (DMDO) to form an epoxide?[1] Here I explore the difference between two different and very simple approaches to predicting its reactivity. bromoallene

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References

  1. D. Christopher Braddock, A. Mahtey, H.S. Rzepa, and A.J.P. White, "Stable bromoallene oxides", Chem. Commun., 2016. http://dx.doi.org/10.1039/C6CC06395K

An alternative mechanism for nucleophilic substitution at silicon using a tetra-alkyl ammonium fluoride.

Friday, May 27th, 2016
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In the previous post, I explored the mechanism for nucleophilic substitution at a silicon centre proceeding via retention of configuration involving a Berry-like pseudorotation. Here I probe an alternative route involving inversion of configuration at the Si centre. Both stereochemical modes are known to occur, depending on the leaving group, solvent and other factors.[1],[2],[3]

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References

  1. L. Wozniak, M. Cypryk, J. Chojnowski, and G. Lanneau, "Optically active silyl esters of phosphorus. II. Stereochemistry of reactions with nucleophiles", Tetrahedron, vol. 45, pp. 4403-4414, 1989. http://dx.doi.org/10.1016/S0040-4020(01)89077-3
  2. L.H. Sommer, and H. Fujimoto, "Stereochemistry of asymmetric silicon. X. Solvent and reagent effects on stereochemistry crossover in alkoxy-alkoxy exchange reactions at silicon centers", Journal of the American Chemical Society, vol. 90, pp. 982-987, 1968. http://dx.doi.org/10.1021/ja01006a024
  3. D.N. Roark, and L.H. Sommer, "Dramatic stereochemistry crossover to retention of configuration with angle-strained asymmetric silicon", Journal of the American Chemical Society, vol. 95, pp. 969-971, 1973. http://dx.doi.org/10.1021/ja00784a081

The mechanism of silylether deprotection using a tetra-alkyl ammonium fluoride.

Wednesday, May 25th, 2016
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The substitution of a nucleofuge (a good leaving group) by a nucleophile at a carbon centre occurs with inversion of configuration at the carbon, the mechanism being known by the term SN2 (a story I have also told in this post). Such displacement at silicon famously proceeds by a quite different mechanism, which I here quantify with some calculations.

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Autoionization of hydrogen fluoride.

Sunday, April 24th, 2016
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The autoionization of water involves two molecules transfering a proton to give hydronium hydroxide, a process for which the free energy of reaction is well known. Here I ask what might happen with the next element along in the periodic table, F.

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Deuteronium deuteroxide. The why of pD 7.435.

Friday, April 22nd, 2016
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Earlier, I constructed a possible model of hydronium hydroxide, or H3O+.OH– One way of assessing the quality of the model is to calculate the free energy difference between it and two normal water molecules and compare the result to the measured difference. Here I apply a further test of the model using isotopes.

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Hydronium hydroxide: the why of pH 7.

Thursday, April 14th, 2016
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Ammonium hydroxide (NH4+…OH) can be characterised quantum mechanically when stabilised by water bridges connecting the ion-pairs. It is a small step from there to hydronium hydroxide, or H3O+…OH. The measured concentrations [H3O+] ≡ [OH] give rise of course to the well-known pH 7 of pure water, and converting this ionization constant to a free energy indicates that the solvated ion-pair must be some ~19.1 kcal/mol higher in free energy than water itself. So can a quantum calculation reproduce pH7 for water?

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Ways to encourage water to protonate an amine: superbasing.

Friday, April 8th, 2016
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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.

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Real hypervalency in a small molecule.

Sunday, February 21st, 2016
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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[1] 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.

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References

  1. 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

Bond stretch isomerism. Did this idea first surface 100 years ago?

Tuesday, February 9th, 2016
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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.[1] Here I explore such isomerism for the elements Ge, Sn and Pb.

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References

  1. 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

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