Archive for the ‘Interesting chemistry’ Category

Imaging vibrational normal modes of a single molecule.

Thursday, April 18th, 2019
No Gravatar

The topic of this post originates from a recent article which is attracting much attention.[1] The technique uses confined light to both increase the spatial resolution by around three orders of magnitude and also to amplify the signal from individual molecules to the point it can be recorded. To me, Figure 3 in this article summarises it nicely (caption: visualization of vibrational normal modes). Here I intend to show selected modes as animated and rotatable 3D models with the help of their calculation using density functional theory (a mode of presentation that the confinement of Figure 3 to the pages of a conventional journal article does not enable).

(more…)

References

  1. J. Lee, K.T. Crampton, N. Tallarida, and V.A. Apkarian, "Visualizing vibrational normal modes of a single molecule with atomically confined light", Nature, vol. 568, pp. 78-82, 2019. http://dx.doi.org/10.1038/s41586-019-1059-9

The Graham reaction: Deciding upon a reasonable mechanism and curly arrow representation.

Monday, February 18th, 2019
No Gravatar

Students learning organic chemistry are often asked in examinations and tutorials to devise the mechanisms (as represented by curly arrows) for the core corpus of important reactions, with the purpose of learning skills that allow them to go on to improvise mechanisms for new reactions. A common question asked by students is how should such mechanisms be presented in an exam in order to gain full credit? Alternatively, is there a single correct mechanism for any given reaction? To which the lecturer or tutor will often respond that any reasonable mechanism will receive such credit. The implication is that a mechanism is “reasonable” if it “follows the rules”. The rules are rarely declared fully, but seem to be part of the absorbed but often mysterious skill acquired in learning the subject. These rules also include those governing how the curly arrows should be drawn. Here I explore this topic using the Graham reaction.[1]

(more…)

References

  1. W.H. Graham, "The Halogenation of Amidines. I. Synthesis of 3-Halo- and Other Negatively Substituted Diazirines1", Journal of the American Chemical Society, vol. 87, pp. 4396-4397, 1965. http://dx.doi.org/10.1021/ja00947a040

“Richer metadata makes content more useful”

Saturday, February 16th, 2019
No Gravatar

The title of this post comes from the site www.crossref.org/members/prep/ Here you can explore how your favourite publisher of scientific articles exposes metadata for their journal.

(more…)

The Chemistry of the Book of Kells

Tuesday, January 22nd, 2019
No Gravatar

The Book of Kells is a spectacularly illuminated gospel manuscript dating from around 800AD and held in Trinity College library in Dublin. Some idea of the colours achieved can be seen below. 

(more…)

Free energy relationships and their linearity: a test example.

Sunday, January 13th, 2019
No Gravatar

Linear free energy relationships (LFER) are associated with the dawn of physical organic chemistry in the late 1930s and its objectives in understanding chemical reactivity as measured by reaction rates and equilibria.

(more…)

Dispersion-induced triplet aromatisation?

Thursday, January 3rd, 2019
No Gravatar

There is emerging interest in cyclic conjugated molecules that happen to have triplet spin states and which might be expected to follow a 4n rule for aromaticity.[1] The simplest such system would be the triplet state of cyclobutadiene, for which a non or anti-aromatic singlet state is always found to be lower in energy. Here I explore some crystal structures containing this motif for possible insights.

(more…)

References

  1. A. Kostenko, B. Tumanskii, Y. Kobayashi, M. Nakamoto, A. Sekiguchi, and Y. Apeloig, "Spectroscopic Observation of the Triplet Diradical State of a Cyclobutadiene", Angewandte Chemie International Edition, vol. 56, pp. 10183-10187, 2017. http://dx.doi.org/10.1002/anie.201705228

Epoxidation of ethene: a new substituent twist.

Friday, December 21st, 2018
No Gravatar

Five years back, I speculated about the mechanism of the epoxidation of ethene by a peracid, concluding that kinetic isotope effects provided interesting evidence that this mechanism is highly asynchronous and involves a so-called “hidden intermediate”. Here I revisit this reaction in which a small change is applied to the atoms involved.

(more…)

Organocatalytic cyclopropanation of an enal: Transition state models for stereoselection.

Sunday, September 30th, 2018
No Gravatar

Here is the concluding part of my exploration of a recently published laboratory experiment for undergraduate students.[1] I had previously outlined a possible mechanistic route, identifying TS3 (below) as the first transition state in which C-C bond formation creates two chiral centres. This is followed by a lower energy TS4 where the final stereocentre is formed, accompanied by inversion of configuration of one of the previously formed centres (red below). Now I explore what transition state calculations have to say about the absolute configurations of the final stereocentres in the carbaldehyde product.

(more…)

References

  1. M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (E)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, vol. 95, pp. 1832-1839, 2018. http://dx.doi.org/10.1021/acs.jchemed.7b00566

Concerted Nucleophilic Aromatic Substitution Mediated by the PhenoFluor Reagent.

Thursday, September 20th, 2018
No Gravatar

Recently, the 100th anniversary of the birth of the famous chemist Derek Barton was celebrated with a symposium. One of the many wonderful talks presented was by Tobias Ritter and entitled “Late-stage fluorination for PET imaging” and this resonated for me. The challenge is how to produce C-F bonds under mild conditions quickly so that 18F-labelled substrates can be injected for the PET imaging. Ritter has several recent articles on this theme which you should read.[1],[2]

(more…)

References

  1. P. Tang, W. Wang, and T. Ritter, "Deoxyfluorination of Phenols", Journal of the American Chemical Society, vol. 133, pp. 11482-11484, 2011. http://dx.doi.org/10.1021/ja2048072
  2. C.N. Neumann, and T. Ritter, "Facile C–F Bond Formation through a Concerted Nucleophilic Aromatic Substitution Mediated by the PhenoFluor Reagent", Accounts of Chemical Research, vol. 50, pp. 2822-2833, 2017. http://dx.doi.org/10.1021/acs.accounts.7b00413

Organocatalytic cyclopropanation of an enal: (computational) assignment of absolute configurations.

Saturday, September 1st, 2018
No Gravatar

I am exploring the fascinating diverse facets of a recently published laboratory experiment for undergraduate students.[1] Previously I looked at a possible mechanistic route for the reaction between an enal (a conjugated aldehyde-alkene) and benzyl chloride catalysed by base and a chiral amine, followed by the use of NMR coupling constants to assign relative stereochemistries. Here I take a look at some chiroptical techniques which can be used to assign absolute stereochemistries (configurations).

(more…)

References

  1. M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (E)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, vol. 95, pp. 1832-1839, 2018. http://dx.doi.org/10.1021/acs.jchemed.7b00566