Posts Tagged ‘Hydrogen bond’

Ammonium tetraphenylborate and the mystery of its π-facial hydrogen bonding.

Friday, March 10th, 2017
No Gravatar

A few years back, I did a post about the Pirkle reagent[1] and the unusual π-facial hydrogen bonding structure[2] it exhibits. For the Pirkle reagent, this bonding manifests as a close contact between the acidic OH hydrogen and the edge of a phenyl ring; the hydrogen bond is off-centre from the middle of the aryl ring. Here I update the topic, with a new search of the CSD (Cambridge structure database), but this time looking at the positional preference of that bond and whether it is on or off-centre. 

(more…)

References

  1. H.S. Rzepa, M.L. Webb, A.M.Z. Slawin, and D.J. Williams, "? Facial hydrogen bonding in the chiral resolving agent (S)-2,2,2-trifluoro-1-(9-anthryl)ethanol and its racemic modification", Journal of the Chemical Society, Chemical Communications, pp. 765, 1991. http://dx.doi.org/10.1039/c39910000765
  2. H.S. Rzepa, M.H. Smith, and M.L. Webb, "A crystallographic AM1 and PM3 SCF-MO investigation of strong OH ⋯π-alkene and alkyne hydrogen bonding interactions", J. Chem. Soc., Perkin Trans. 2, pp. 703-707, 1994. http://dx.doi.org/10.1039/P29940000703

The “hydrogen bond”; its early history.

Saturday, December 31st, 2016
No Gravatar

My holiday reading has been Derek Lowe’s excellent Chemistry Book setting out 250 milestones in chemistry, organised by year. An entry for 1920 entitled hydrogen bonding seemed worth exploring in more detail here.

(more…)

Hydrogen bonding to chloroform.

Monday, November 14th, 2016
No Gravatar

Chloroform, often in the deuterated form CDCl3, is a very common solvent for NMR and other types of spectroscopy. Quantum mechanics is increasingly used to calculate such spectra to aid assignment and the solvent is here normally simulated as a continuum rather than by explicit inclusion of one or more chloroform molecules. But what are the features of the hydrogen bonds that form from chloroform to other acceptors? Here I do a quick search for the common characteristics of such interactions.

(more…)

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

Monday, August 8th, 2016
No Gravatar

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:

(more…)

How does an OH or NH group approach an aromatic ring to hydrogen bond with its π-face?

Wednesday, June 22nd, 2016
No Gravatar

I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and OH or NH groups.

(more…)

Autoionization of hydrogen fluoride.

Sunday, April 24th, 2016
No Gravatar

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.

(more…)

Oxane oxide: a tautomer of hydrogen peroxide.

Friday, April 15th, 2016
No Gravatar

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

(more…)

Azane oxide, a tautomer of hydroxylamine.

Friday, April 15th, 2016
No Gravatar

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).

(more…)

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
No Gravatar

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?

(more…)

Ways to encourage water to protonate an amine: superbasing.

Friday, April 8th, 2016
No Gravatar

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.

(more…)