Henry Rzepa's Blog Chemistry with a twist

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

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 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


January 3, 2013

Hydrogen bond strength as a function of ring size.

Filed under: Interesting chemistry — Tags: , , , , — Henry Rzepa @ 4:48 pm

One frequently has to confront the question: will a hydrogen bond form between a suitable donor (lone pair or π) and an acceptor? One of the factors to be taken into consideration for hydrogen bonds which are part of a cycle is the ring size. Here I explore one way of quantifying the effect for the series below, n=1-5 (4-8 membered rings).


September 12, 2012

What is the range of values for a (sp3)C-C(sp3) single bond length?

Filed under: Interesting chemistry — Tags: , — Henry Rzepa @ 4:11 pm

Here is a challenge: what is the longest C-C bond actually determined (in which both carbon termini are sp3 hybridised)? I pose this question since Steve Bachrach has posted on how to stabilize long bonds by attractive dispersive interactions, and more recently commenting on what the longest straight chain alkane might be before dispersive interaction start to fold it (the answer appears to be C17).


July 19, 2012

Dynamic effects in nucleophilic substitution at trigonal carbon (with Na+).

Filed under: Uncategorised — Tags: , , , — Henry Rzepa @ 1:43 pm

In the preceding post, I described a fascinating experiment and calculation by Bogle and Singleton, in which the trajectory distribution of molecules emerging from a single transition state was used to rationalise the formation of two isomeric products 2 and 3.  In the present post, I explore possible consequences of including a sodium cation (X=Na+ below) in the computational model.


July 12, 2012

More joining up of pieces. Stereocontrol in the ring opening of cyclopropenes.

Years ago, I was travelling from Cambridge to London on a train. I found myself sitting next to a chemist, and (as chemists do), he scribbled the following on a piece of paper. When I got to work the next day Vera (my student) was unleashed on the problem, and our thoughts were published[1]. That was then.



  1. M.S. Baird, J.R. Al Dulayymi, H.S. Rzepa, and V. Thoss, "An unusual example of stereoelectronic control in the ring opening of 3,3-disubstituted 1,2-dichlorocyclopropenes", Journal of the Chemical Society, Chemical Communications, pp. 1323, 1992. http://dx.doi.org/10.1039/C39920001323

July 6, 2011

Scalemic molecules: a cheminformatics challenge!

A scalemic molecule is the term used by Eliel to describe any non-racemic chiral compound. Synthetic chemists imply it when they describe a synthetic product with an observable enantiomeric excess or ee (which can range from close to 0% to almost 100%). There are two cheminformatics questions of interest to me: (more…)

May 31, 2011

Déjà vu all over again. Are H…H interactions attractive or repulsive?

Filed under: Interesting chemistry — Tags: , , , , — Henry Rzepa @ 6:51 am

The Pirkle reagent is a 9-anthranyl derivative (X=OH, Y=CF3). The previous post on the topic had highlighted DIST1, the separation of the two hydrogen atoms shown below. The next question to ask is how general this feature is. Here we take a look at the distribution of lengths found in the Cambridge data base, and focus on another interesting example.


April 25, 2011

Beryllocene and Uranocene: The 8, 18 and 32-electron rules.

Filed under: Interesting chemistry — Tags: , , , , , , — Henry Rzepa @ 8:19 am

In discussing ferrocene in the previous post, I mentioned Irving Langmuir’s 1921 postulate that filled valence shells in what he called complete molecules would have magic numbers of 2, 8, 18 or 32 electrons (deriving from the sum of terms in 2[1+3+5+7]). The first two dominate organic chemistry of course, whilst the third is illustrated by the transition series, ferrocene being an example of such. The fourth case is very much rarer, only one example ever having been suggested[1], it deriving from the actinides. In this post, I thought I would augment ferrocene (an 18-electron example) with beryllocene (an 8-electron example) and then speculate about 32-electron metallocenes.



  1. J. Dognon, C. Clavaguéra, and P. Pyykkö, "Towards a 32-Electron Principle: Pu@Pb12 and Related Systems", Angewandte Chemie International Edition, vol. 46, pp. 1427-1430, 2007. http://dx.doi.org/10.1002/anie.200604198
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