Henry Rzepa's Blog Chemistry with a twist

March 17, 2013

The mysterious (aromatic) structure of n-Butyl lithium.

n-Butyl lithium is hexameric in the solid state[1] and in cyclohexane solutions. Why? Here I try to find out some of its secrets.



  1. T. Kottke, and D. Stalke, "Structures of Classical Reagents in Chemical Synthesis:(nBuLi)6,(tBuLi)4, and the Metastable(tBuLi· Et2O)2", Angewandte Chemie International Edition in English, vol. 32, pp. 580-582, 1993. http://dx.doi.org/10.1002/anie.199305801

February 21, 2013

A to-and-fro of electrons operating in s-cis esters.

I conclude my exploration of conformational preferences by taking a look at esters. As before, I start with a search definition, the ester being restricted to one bearing only sp3 carbon centers.


February 11, 2013

The conformational preference of s-cis amides. Ramachandran plots.

Filed under: Interesting chemistry — Tags: , , — Henry Rzepa @ 6:16 pm

This is really just a postscript to the previous post. There I showed how a search of the (small molecule) crystal database revealed the s-cis conformation about the N-C amide bond (the one with partial double bond character that prevents rotation) and how this conformation means that a C-H approaches quite closely to an adjacent oxygen. It is a tiny step from that search to a related, and very famous one named after Ramachandran[1]. Indeed this search, and the contour map used to display the results, really put crystal databases on the map so to speak.



  1. G. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, "Stereochemistry of polypeptide chain configurations", Journal of Molecular Biology, vol. 7, pp. 95-99, 1963. http://dx.doi.org/10.1016/S0022-2836(63)80023-6

February 10, 2013

The conformational preference of s-cis amides.

Amides with an H-N group are a component of the peptide linkage (O=C-NH). Here I ask what the conformation (it could also be called a configuration) about the C-N bond is. A search of the following type can be defined:


February 8, 2013

The conformation of acetaldehyde: a simple molecule, a complex explanation?

Consider acetaldehyde (ethanal for progressive nomenclaturists). What conformation does it adopt, and why? This question was posed of me by a student at the end of a recent lecture of mine. Surely, an easy answer to give? Read on …


February 3, 2013

Secrets of a university tutor: conformational analysis and NMR spectroscopy.

Filed under: Uncategorised — Tags: , , , — Henry Rzepa @ 2:10 pm

In a previous post, I set out how to show how one can reduce a 1H NMR spectrum to the structure [A] below. I speculated how a further test could be applied to this structure; back predicting its spectrum using just quantum mechanics. Overkill I know, but how well might the two match?


σ-π-Conjugation: seeking evidence by a survey of crystal structures.

The electronic interaction between a single bond and an adjacent double bond is often called σ-π-conjugation (an older term for this is hyperconjugation), and the effect is often used to e.g. explain why more highly substituted carbocations are more stable than less substituted ones. This conjugation is more subtle in neutral molecules, but following my use of crystal structures to explore the so-called gauche effect (which originates from σ-σ-conjugation), I thought I would have a go here at seeing what the crystallographic evidence actually is for the σ-π-type.


January 13, 2013

The strangely attractive conformation of C17H36.

Filed under: Uncategorised — Tags: , , — Henry Rzepa @ 9:15 am

We tend to think of simple hydrocarbons as relatively inert and un-interesting molecules. However, a recent article[1], which was in fact highlighted by Steve Bachrach on his blog , asks what “The Last Globally Stable Extended Alkane” might be. In other words, at what stage does a straight-chain hydrocarbon fold back upon itself, and no significant population of the linear form remain? The answer was suggested to be C17H36. I thought I might subject this conformation to an NCI (non-covalent-interaction) analysis.



  1. N.O.B. Lüttschwager, T.N. Wassermann, R.A. Mata, and M.A. Suhm, "The Last Globally Stable Extended Alkane", Angewandte Chemie International Edition, vol. 52, pp. 463-466, 2012. http://dx.doi.org/10.1002/anie.201202894

January 10, 2013

A conflation of concepts: Conformation and pericyclic.

Filed under: Uncategorised — Tags: , , , , — Henry Rzepa @ 11:09 am

This is an interesting result I got when studying the [1,4] sigmatropic rearrangement of heptamethylbicyclo-[3.1.0]hexenyl cations. It fits into the last lecture of a series on pericyclic mechanisms, and just before the first lecture on conformational analysis. This is how they join.


January 4, 2013

The gauche effect: seeking evidence by a survey of crystal structures.

I previously blogged about anomeric effects involving π electrons as donors, and my post on the conformation of 1,2-difluorethane turned out one of the most popular. Here I thought I would present the results of searching the Cambridge crystal database for examples of the gauche effect. The basic search is defined belowCCDC-search


Older Posts »

Powered by WordPress