Archive for the ‘Interesting chemistry’ Category

More stereoelectronics galore: hexamethylene triperoxide diamine.

Thursday, September 22nd, 2016
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Compounds with O-O bonds often have weird properties. For example, artemisinin, which has some fascinating stereoelectronics. Here is another such, recently in the news and known as HMTD (hexamethylene triperoxide diamine). The crystal structure was reported some time ago[1] and the article included an inspection of the computed wavefunction. However this did not look at the potential stereoelectronics in this species, which I now address here.

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References

  1. A. Wierzbicki, E.A. Salter, E.A. Cioffi, and E.D. Stevens, "Density Functional Theory and X-ray Investigations of P- and M-Hexamethylene Triperoxide Diamine and Its Dialdehyde Derivative", J. Phys. Chem. A, vol. 105, pp. 8763-8768, 2001. http://dx.doi.org/10.1021/jp0123841

A periodic table for anomeric centres, this time with quantified interactions.

Monday, August 8th, 2016
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The previous post contained an exploration of the anomeric effect as it occurs at an atom centre X for which the effect is manifest in crystal structures. Here I quantify the effect, by selecting the test molecule MeO-X-OMe, where X is of two types:

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A periodic table for anomeric centres.

Saturday, August 6th, 2016
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In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. Here I try to summarise the atoms for which the effect is manifest in crystal structures.

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Stereoelectronic effects galore: bis(trifluoromethyl)trioxide.

Thursday, August 4th, 2016
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Here is a little molecule that can be said to be pretty electron rich. There are lots of lone pairs present, and not a few electron-deficient σ-bonds. I thought it might be fun to look at the stereoelectronic interactions set up in this little system.

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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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Oxane oxide: a tautomer of hydrogen peroxide.

Friday, April 15th, 2016
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If H3N+-O is viable compared with its tautomer H2N-OH when carrying water bridges, then why not try H2O+-O vs HO-OH?

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Azane oxide, a tautomer of hydroxylamine.

Friday, April 15th, 2016
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In the previous post I described how hydronium hydroxide or H3O+…HO, an intermolecular tautomer of water, has recently been observed captured inside an organic cage[1] and how the free-standing species in water can be captured computationally with the help of solvating water bridges. Here I explore azane oxide or H3N+-O, a tautomer of the better known hydroxylamine (H2N-OH).

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References

  1. M. Stapf, W. Seichter, and M. Mazik, "Unique Hydrogen-Bonded Complex of Hydronium and Hydroxide Ions", Chemistry - A European Journal, vol. 21, pp. 6350-6354, 2015. http://dx.doi.org/10.1002/chem.201406383

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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