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.
Posts Tagged ‘chemical bonding’
How does an OH or NH group approach an aromatic ring to hydrogen bond with its π-face?
Wednesday, June 22nd, 2016Hydronium hydroxide: the why of pH 7.
Thursday, April 14th, 2016Ammonium 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?
Real hypervalency in a small molecule.
Sunday, February 21st, 2016Hypervalency 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.
References
- 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
VSEPR Theory: A closer look at trifluorothionitrile, NSF3.
Saturday, January 16th, 2016The post on applying VSEPR ("valence shell electron pair repulsion") theory to the geometry of ClF3 has proved perennially popular. So here is a follow-up on another little molecue, F3SN. As the name implies, it is often represented with an S≡N bond. Here I take a look at the conventional analysis.
Interactions responsible for the lowest energy structure of the trimer of fluoroethanol.
Friday, October 23rd, 2015Steve Bachrach on his own blog has commented on a recent article[1] discussing the structure of the trimer of fluoroethanol. Rather than the expected triangular form with three OH—O hydrogen bonds, the lowest energy form only had two such bonds, but it matched the microwave data much better. Here I explore this a bit more.
References
- J. Thomas, X. Liu, W. Jäger, and Y. Xu, "Unusual H‐Bond Topology and Bifurcated H‐bonds in the 2‐Fluoroethanol Trimer", Angewandte Chemie International Edition, vol. 54, pp. 11711-11715, 2015. http://dx.doi.org/10.1002/anie.201505934
π-Resonance in amides: a crystallographic reality check.
Saturday, September 5th, 2015The π-resonance in amides famously helped Pauling to his proposal of a helical structure for proteins. Here I explore some geometric properties of amides related to the C-N bond and the torsions about it.
Mesomeric resonance in substituted benzenes: a crystallographic reality check.
Wednesday, August 26th, 2015Previously, I showed how conjugation in dienes and diaryls can be visualised by inspecting bond lengths as a function of torsions. Here is another illustration, this time of the mesomeric resonance on a benzene ring induced by an electron donating substituent (an amino group) or an electron withdrawing substituent (cyano).