Introductory organic chemistry invariably features the mechanism of haloalkane solvolysis, and introduces both the Sn1 two-step mechanism, and the Sn2 one step mechanism to students. They are taught to balance electronic effects (the stabilization of carbocations) against steric effects in order to predict which mechanism prevails. It was whilst preparing a tutorial on this topic that I came across what was described as the special case of neopentyl bromide, the bimolecular solvolysis of which has been identified (DOI: 10.1021/ja01182a117) as being as much as 3 million times slower than methyl bromide. This is attributed to a very strong steric effect on the reaction, greater even than that which might be experienced by t-butyl bromide! Time I thought, to take a look at what might make neopentyl bromide so special, and what those supposed electronic and steric effects were really up to.
Nobelocene: a (hypothetical) 32-electron shell molecule?
April 29th, 2011The two previous posts have explored one of the oldest bonding rules (pre-dating quantum mechanics), which postulated that filled valence shells in atoms forming molecules follow the magic numbers 2, 8, 18 and 32. Of the 59,025,533 molecules documented at the instant I write this post, only one example is claimed for the 32-electron class. Here I suggest another, Nobelocene (one which given the radioactive instability of nobelium, is unlikely to be ever confirmed experimentally!)
Ferrocene
April 17th, 2011
The structure of ferrocene was famously analysed by Woodward and Wilkinson in 1952[cite]10.1021/ja01128a527[/cite],[cite]10.1016/S0022-328X(00)88947-0[/cite], symmetrically straddled in history by Pauling (1951) and Watson and Crick (1953). Quite a trio of Nobel-prize winning molecular structural analyses, all based on a large dose of intuition. The structures of both proteins and DNA succumbed to models built from simple Lewis-type molecules with covalent (and hydrogen) bonds; ferrocene is intriguingly similar and yet different. Similar because
Why are α-helices in proteins mostly right handed?
April 9th, 2011Understanding why and how proteins fold continues to be a grand challenge in science. I have described how Wrinch in 1936 made a bold proposal for the mechanism, which however flew in the face of much of then known chemistry. Linus Pauling took most of the credit (and a Nobel prize) when in a famous paper[cite]10.1073/pnas.37.4.205[/cite] in 1951 he suggested a mechanism that involved (inter alia) the formation of what he termed α-helices. Jack Dunitz in 2001[cite]10.1002/1521-3773(20011119)40:22%3C4167::AID-ANIE4167%3E3.0.CO;2-Q[/cite] wrote a must-read article[cite]10.fgkwqb[/cite] on the topic of “Pauling’s Left-handed α-helix” (it is now known to be right handed). I thought I would revisit this famous example with a calculation of my own and here I have used the ωB97XD/6-311G(d,p) DFT procedure[cite]10.1021/ct100469b[/cite] to calculate some of the energy components of a small helix comprising (ala)6 in both left and right handed form.
The colour of Monastral blue (part 2).
April 4th, 2011Andy Mclean posted a comment to my story of copper phthalocyanine (Monastral blue). The issue was its colour, and more specifically why this pigment has two peaks λmax 610 and 710nm making it blue. The first was accurately reproduced by calculation on the monomer, but the second was absent with such a model. Andy suggested this latter was due to stacking. Here, the calculated spectrum of a stacked dimer is explored.
Chemicalizing a blog.
March 30th, 2011I am at the ACS meeting, attending a session on chemistry and the Internet. This post was inspired by Chemicalize, a service offered by ChemAxon, which scans a post like this one, and identifies molecules named. I had previously used generic post taggers, which frankly did not work well in identifying chemical content. So this is by way of an experiment. I list below some of the substances about which I have blogged, to see how the chemicalizer works. Read the rest of this entry »
From the colour blue to molecular wires
March 9th, 2011In the previous post I pondered the colour of Monastral blue (copper phthalocyanine). Something did not quite fit, and so I speculated that perhaps some oxidation of the pigment might give a new species. This species (Cambridge code FEGJOQ) comprises two parts of copper phthalocyanine, 1 part of the corresponding cation, and 1 part of triodide anion. Looking at the packing of this system, I spotted something I had seen some time ago in NaI2.Acetone, namely an infinitely long and absolutely straight chain of iodine atoms, a molecular wire if you like.