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.
What is the best way of folding a straight chain alkane?
April 6th, 2014Modelling the geometry of unbranched alkanes.
March 29th, 2014By about C17H36, the geometry of “cold-isolated” unbranched saturated alkenes is supposed not to contain any fully anti-periplanar conformations. [cite]10.1002/anie.201202894[/cite] Indeed, a (co-crystal) of C16H34 shows it to have two-gauche bends.[cite]10.1002/chem.200801428[/cite]. Surprisingly, the longest linear alkane I was able to find a crystal structure for, C28H58 appears to be fully extended[cite]10.1107/S0108768191011059[/cite],[cite]10.1107/S0567740876005025[/cite] (an early report of a low quality structure for C36H74[cite]10.1107/S0365110X5600111X[/cite] also appears to show it as linear).‡ Here I explore how standard DFT theories cope with these structures.
Five things you did not know about (fork) handles.
March 18th, 2014OK, you have to be British to understand the pun in the title, a famous comedy skit about four candles. Back to science, and my mention of some crystal data now having a DOI in the previous post. I thought it might be fun to replicate the contents of one of my ACS slides here.
The Amsterdam Manifesto and crystal structures.
March 18th, 2014I have mentioned the Amsterdam manifesto before on these pages. It is worth repeating the eight simple principles:
Happy 25th birthday, WWW.
March 12th, 2014A 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.
The mechanism of diazo coupling: more hidden mechanistic intermediates.
March 8th, 2014The diazo-coupling reaction dates back to the 1850s (and a close association with Imperial College via the first professor of chemistry there, August von Hofmann) and its mechanism was much studied in the heyday of physical organic chemistry.[cite]10.1021/ja00830a009[/cite] Nick Greeves, purveyor of the excellent ChemTube3D site, contacted me about the transition state (I have commented previously on this aspect of aromatic electrophilic substitution). ChemTube3D recruits undergraduates to add new entries; Blue Jenkins is one such adding a section on dyes.
The wrong trousers: the anti-Markovnikov addition of borane to 2-methylpropene.
March 2nd, 2014A staple of introductory undergraduate teaching in organic chemistry is Markovnikov’s rule, which states: “the addition of a protic acid HX to an alkene results in the acid hydrogen (H) becoming attached to the carbon with fewer alkyl substituents and the halide (X) group to the carbon with more alkyl substituents“. Shortly thereafter, students are exposed to the “anti-Markovnikov” addition of borane to e.g. 2-methylpropene. In order to achieve a consistent explanation for both reactions, I normally show students the following mechanism. Here I introduce a “reality check” to the first component of that mechanism (for the oxidative step, see this post).
Intersecting paths in molecular energy surfaces.
February 16th, 2014The potential energy surface for a molecule tells us about how it might react. These surfaces have been charted for thousands of reactions using quantum mechanics, and their basic features are thought to be well understood. Coming across an entirely new feature is rare. So what do you make of the following?
A congruence of concepts: conformations, configurations, amides and enzymes
February 9th, 2014This 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.