Archive for the ‘General’ Category

What is the best way of folding a straight chain alkane?

Sunday, April 6th, 2014

In the previous post, I showed how modelling of unbranched alkenes depended on dispersion forces. When these are included, a bent (single-hairpin) form of C58H118 becomes lower in free energy than the fully extended linear form. Here I try to optimise these dispersion forces by adding further folds to see what happens.


Modelling the geometry of unbranched alkanes.

Saturday, March 29th, 2014

By about C17H36, the geometry of “cold-isolated” unbranched saturated alkenes is supposed not to contain any fully anti-periplanar conformations. [1] Indeed, a (co-crystal) of C16H34 shows it to have two-gauche bends.[2]. Surprisingly, the longest linear alkane I was able to find a crystal structure for, C28H58 appears to be fully extended[3],[4] (an early report of a low quality structure for C36H74[5] also appears to show it as linear). Here I explore how standard DFT theories cope with these structures.



  1. N.O.B. Lüttschwager, T.N. Wassermann, R.A. Mata, and M.A. Suhm, "The Last Globally Stable Extended Alkane", Angew. Chem. Int. Ed., vol. 52, pp. 463-466, 2013.
  2. N. Cocherel, C. Poriel, J. Rault-Berthelot, F. Barrière, N. Audebrand, A.M.Z. Slawin, and L. Vignau, "New 3π-2Spiro Ladder-Type Phenylene Materials: Synthesis, Physicochemical Properties and Applications in OLEDs", Chemistry - A European Journal, vol. 14, pp. 11328-11342, 2008.
  3. S.C. Nyburg, and A.R. Gerson, "Crystallography of the even n-alkanes: structure of C20H42", Acta Cryst Sect B, vol. 48, pp. 103-106, 1992.
  4. R. Boistelle, B. Simon, and G. Pèpe, "Polytypic structures of n-C28H58 (octacosane) and n-C36H74 (hexatriacontane)", Acta Crystallographica Section B Structural Crystallography and Crystal Chemistry, vol. 32, pp. 1240-1243, 1976.
  5. H.M.M. Shearer, and V. Vand, "The crystal structure of the monoclinic form of n-hexatriacontant", Acta Crystallographica, vol. 9, pp. 379-384, 1956.

Happy 25th birthday, WWW.

Wednesday, March 12th, 2014

A short post this, to remind that today is officially the 25th birthday of the World-Wide-Web, in March 1989. It took five years for a conference around the theme to be organised and below is a photo from that event.


A congruence of concepts: conformations, configurations, amides and enzymes

Sunday, February 9th, 2014

This is the time of year when I deliver two back-2-back lecture courses, and yes I do update and revise the content! I am always on the look-out for nice new examples that illustrate how concepts and patterns in chemistry can be joined up to tell a good story. My attention is currently on conformational analysis; and here is an interesting new story to tell about it.


3D-rendered molecular models on this blog: an update.

Thursday, January 16th, 2014

So much to do, so little time to do it. That is my excuse at least. Right from my first post on this blog in 2008 I have tried to enhance it using Jmol, a Java-based applet (normally indicated with the caption Click for 3D). This has been pretty stable for some five years now, but a recent spate of security-based releases of the JRE (Java runtime environment) for desktop computers has impacted, the latest of which was released yesterday (Java 7, V 51).  Put simply, when I started, an unsigned applet was fine. Now to run, it can only be a properly signed applet. Fortunately, there are two solutions:


Refactoring my lecture notes on pericyclic reactions.

Sunday, December 29th, 2013

When I first started giving lectures to students, it was the students themselves that acted as human photocopiers, faithfully trying to duplicate what I was embossing on the lecture theatre blackboard with chalk. How times have changed! Here I thought I might summarise my latest efforts to refactor the material I deliver in one lecture course on pericyclic reactions (and because my notes have always been open, you can view them yourself if you wish).


A curly-arrow pushing manual

Wednesday, December 4th, 2013

I have several times used arrow pushing on these blogs. But since the rules for this convention appear to be largely informal, and there appears to be no definitive statement of them, I thought I would try to produce this for our students. This effort is here shared on my blog. It is what I refer to as the standard version; an advanced version is in preparation. Such formality might come as a surprise to some; arrow-pushing is often regarded as far too approximate to succumb to any definition, although it is of course often examined.


Blasts from the past and present: altmetrics.

Sunday, October 13th, 2013

I reminisced about the wonderfully naive but exciting Web-period of 1993-1994. This introduced the server-log analysis to us for the first time, and hits-on-a-web-page. One of our first attempts at crowd-sourcing and analysis was to run an electronic conference in heterocyclic chemistry and to look at how the attendees visited the individual posters and presentations by analysing the server logs.


The demographics of a blog readership.

Sunday, January 20th, 2013

With metrics in science publishing controversial to say the least, I pondered whether to write about the impact/influence a science-based blog might have (never mind whether it constitutes any measure of esteem). These are all terms that feature large when an (academic) organisation undertakes a survey of its researchers’ effectiveness. WordPress (the organisation that provides the software used for this blog) recently enhanced the stats it offers for its users, and one of these caught my eye.


Transition state models for Baldwin’s rules of ring closure.

Saturday, June 2nd, 2012

The Baldwin rules for ring closure follow the earlier ones by Bürgi and Dunitz in stating the preferred angles of nucleophilic (and electrophilic) attack in bond forming reactions, and are as famous for the interest in their exceptions as for their adherence. Both sets of rules fundamentally explore the geometry of the transition states involved in the reaction, as reflected in the activation free energies. Previous posts exploring the transition states for well-known reactions have revealed that the 4th dimension (the timing of the bond formations/breakings) can often spring surprises. So this post will explore a typical Baldwin ring formation in the same way.