William Henry Perkin is a local chemical hero of mine. The factory where he founded the British (nay, the World) fine organic chemicals industry is in Greenford, just up the road from where we live. The factory used to be close to the Black Horse pub (see below) on the banks of the grand union canal. It is now commemorated merely by a blue plaque placed on the wall of the modern joinery building occupying the location (circled in red on the photo).
William Henry Perkin: The site of the factory and the grave.
March 11th, 2013Kinetic vs Thermodynamic control. Subversive thoughts for electrophilic substitution of Indole.
March 10th, 2013I mentioned in the last post that one can try to predict the outcome of electrophilic aromatic substitution by approximating the properties of the transition state from those of either the reactant or the (presumed Wheland) intermediate by invoking Hammond’s postulate[1]. A third option is readily available nowadays; calculate the transition state directly. Here are the results of exploring this third variation.
References
- G.S. Hammond, "A Correlation of Reaction Rates", Journal of the American Chemical Society, vol. 77, pp. 334-338, 1955. https://doi.org/10.1021/ja01607a027
Understanding the electrophilic aromatic substitution of indole.
March 3rd, 2013The electrophilic substitution of indoles is a staple of any course on organic chemistry. Indoles also hold a soft-spot for me, since I synthesized not a few as part of my Ph.D. studies.[1],[2] The preference for substitution in the 3-position is normally explained using the arrows shown below (position 3=green,2=blue,1=red). Here I explore how these arrows might be interpreted in terms of various quantum mechanical properties.
References
- B.C. Challis, and H.S. Rzepa, "The mechanism of diazo-coupling to indoles and the effect of steric hindrance on the rate-limiting step", Journal of the Chemical Society, Perkin Transactions 2, pp. 1209, 1975. https://doi.org/10.1039/p29750001209
- B.C. Challis, and H.S. Rzepa, "Heteroaromatic hydrogen exchange reactions. Part 9. Acid catalysed decarboxylation of indole-3-carboxylic acids", Journal of the Chemical Society, Perkin Transactions 2, pp. 281, 1977. https://doi.org/10.1039/p29770000281
Why is the carbonyl IR stretch in an ester higher than in a ketone?
February 28th, 2013Infra-red spectroscopy of molecules was introduced 110 years ago by Coblentz[1] as the first functional group spectroscopic method (” The structure of the compound has a great influence on the absorption spectra. In many cases it seems as though certain bonds are due to certain groups.“). It hangs on in laboratories to this day as a rapid and occasionally valuable diagnostic tool, taking just minutes to measure. Its modern utility rests on detecting common functional groups, mostly based around identifying the nature of double or triple bonds, and to a lesser extent in differentiating between different kinds of C-H stretches[2] (and of course OH and NH). One common use is to identify the environment of carbonyl groups, C=O. These tend to come in the form of aldehydes and ketones, esters, amides, acyl halides, anhydrides and carbonyls which are part of small rings. The analysis is performed by assigning the value of the C=O stretching wavenumber to a particular range characteristic of each type of compound. Thus ketones are said to inhabit the range of ~1715-1740 cm-1 and simple esters come at ~1740-1760 cm-1, some 20-30 cm-1 higher. Here I try to analyse how this difference arises.
References
- W.W. Coblentz, "Infra-red Absorption Spectra: I. Gases", Physical Review (Series I), vol. 20, pp. 273-291, 1905. https://doi.org/10.1103/physrevseriesi.20.273
- J.L. Arbour, H.S. Rzepa, J. Contreras‐García, L.A. Adrio, E.M. Barreiro, and K.K.(. Hii, "Silver‐Catalysed Enantioselective Addition of OH and NH Bonds to Allenes: A New Model for Stereoselectivity Based on Noncovalent Interactions", Chemistry – A European Journal, vol. 18, pp. 11317-11324, 2012. https://doi.org/10.1002/chem.201200547
A to-and-fro of electrons operating in s-cis esters.
February 21st, 2013I conclude my exploration of conformational preferences by taking a look at esters. As before, I start with a search definition, the ester being restricted to one bearing only sp3 carbon centers.
Linking numbers, and twist and writhe components for two extended porphyrins.
February 17th, 2013My last comment as appended to the previous post promised to analyse two so-called extended porphyrins for their topological descriptors. I start with the Cãlugãreanu/Fuller theorem which decomposes the topology of a space curve into two components, its twist (Tw) and its writhe (Wr, this latter being the extent to which coiling of the central curve has relieved local twisting) and establishes a topological invariant called the linking number[1]
References
- S.M. Rappaport, and H.S. Rzepa, "Intrinsically Chiral Aromaticity. Rules Incorporating Linking Number, Twist, and Writhe for Higher-Twist Möbius Annulenes", Journal of the American Chemical Society, vol. 130, pp. 7613-7619, 2008. https://doi.org/10.1021/ja710438j
Helically conjugated molecules. A follow-up to [144]-annulene.
February 12th, 2013An extensive discussion developed regarding my post on a fascinating helical [144]-annulene. Topics included the nature of the ring current sustained by the π-electrons and in particular the bond-length alternation around the periphery and whether this should alter if the electron count were to be changed to that of a 4n+2 system (i.e. a dication). Whilst the [144]-annulene itself is hypothetical, it emerged that some compounds known as expanded porphyrins have very similar (albeit smaller scale) helical structures. X-ray structures for two such provide useful reality checks on the calculations. Here‡ I include the (3D) coordinates of these two systems so that you can explore for yourself their helicity.
The conformational preference of s-cis amides. Ramachandran plots.
February 11th, 2013This is really just a postscript to the previous post. There I showed how a search of the (small molecule) crystal database revealed the s-cis conformation about the N-C amide bond (the one with partial double bond character that prevents rotation) and how this conformation means that a C-H approaches quite closely to an adjacent oxygen. It is a tiny step from that search to a related, and very famous one named after Ramachandran[1]. Indeed this search, and the contour map used to display the results, really put crystal databases on the map so to speak.
References
- G. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, "Stereochemistry of polypeptide chain configurations", Journal of Molecular Biology, vol. 7, pp. 95-99, 1963. https://doi.org/10.1016/s0022-2836(63)80023-6
The conformational preference of s-cis amides.
February 10th, 2013Amides with an H-N group are a component of the peptide linkage (O=C-NH). Here I ask what the conformation (it could also be called a configuration) about the C-N bond is. A search of the following type can be defined:
The conformation of acetaldehyde: a simple molecule, a complex explanation?
February 8th, 2013Consider acetaldehyde (ethanal for progressive nomenclaturists). What conformation does it adopt, and why? This question was posed of me by a student at the end of a recent lecture of mine. Surely, an easy answer to give? Read on …