This molecule is not leaving me in peace. It and I first met in 1990 (DO: 10.1039/C39910000765), when we spotted the two unusual π-facial bonds formed when it forms a loose dimer. The next step was to use QTAIM to formalise this interaction, and this led to spotting a second one missed the first time round (labelled 2 in that post). Then a method known as NCI was tried, which revealed an H…H interaction, labelled ? in that post! Here I discuss the origins of the ?
Déjà vu: Pirkle for a third time!
May 25th, 2011The inner secrets of the DNA structure.
May 18th, 2011In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets.
Updating a worked problem in conformational analysis. Part 2: an answer.
May 17th, 2011The previous post set out a problem in conformational analysis. Here is my take, which includes an NCI (non-covalent interaction) display as discussed in another post.
Updating a worked problem in conformational analysis. Part 1: the question.
May 13th, 2011Conformational analysis comes from the classical renaissance of physical organic chemistry in the 1950s and 60s. The following problem is taken from E. D. Hughes and J. Wilby J. Chem. Soc., 1960, 4094-4101, DOI: 10.1039/JR9600004094, the essence of which is that Hofmann elimination of a neomenthyl derivative (C below) was observed as anomalously faster than its menthyl analogue. Of course, what is anomalous in one decade is a standard student problem (and one Nobel prize) five decades later.
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[1],[2], 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
References
- G. Wilkinson, M. Rosenblum, M.C. Whiting, and R.B. Woodward, "THE STRUCTURE OF IRON BIS-CYCLOPENTADIENYL", Journal of the American Chemical Society, vol. 74, pp. 2125-2126, 1952. https://doi.org/10.1021/ja01128a527
- G. Wilkinson, "The iron sandwich. A recollection of the first four months", Journal of Organometallic Chemistry, vol. 100, pp. 273-278, 1975. https://doi.org/10.1016/s0022-328x(00)88947-0
- I. Langmuir, "Types of Valence", Science, vol. 54, pp. 59-67, 1921. https://doi.org/10.1126/science.54.1386.59
- J. Dognon, C. Clavaguéra, and P. Pyykkö, "Towards a 32‐Electron Principle: Pu@Pb<sub>12</sub> and Related Systems", Angewandte Chemie International Edition, vol. 46, pp. 1427-1430, 2007. https://doi.org/10.1002/anie.200604198
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[1] in 1951 he suggested a mechanism that involved (inter alia) the formation of what he termed α-helices. Jack Dunitz in 2001[2] wrote a must-read article[3] 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[4] to calculate some of the energy components of a small helix comprising (ala)6 in both left and right handed form.
References
- L. Pauling, R.B. Corey, and H.R. Branson, "The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain", Proceedings of the National Academy of Sciences, vol. 37, pp. 205-211, 1951. https://doi.org/10.1073/pnas.37.4.205
- J.D. Dunitz, "Pauling's Left-Handed α-Helix", Angewandte Chemie International Edition, vol. 40, pp. 4167-4173, 2001. https://doi.org/10.1002/1521-3773(20011119)40:22<4167::aid-anie4167>3.0.co;2-q
- https://doi.org/
- K.S. Thanthiriwatte, E.G. Hohenstein, L.A. Burns, and C.D. Sherrill, "Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded Interactions", Journal of Chemical Theory and Computation, vol. 7, pp. 88-96, 2010. https://doi.org/10.1021/ct100469b