The 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.[cite]10.1039/P29750001209[/cite],[cite]10.1039/P29770000281[/cite] 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.
Understanding the electrophilic aromatic substitution of indole.
March 3rd, 2013Why 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[cite]10.1103/PhysRevSeriesI.20.273[/cite] 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[cite]10.1002/chem.201200547[/cite] (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.
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[cite]10.1021/ja710438j[/cite]
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[cite]10.1016/S0022-2836(63)80023-6[/cite]. Indeed this search, and the contour map used to display the results, really put crystal databases on the map so to speak.
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 …
Secrets of a university tutor: conformational analysis and NMR spectroscopy.
February 3rd, 2013In a previous post, I set out how to show how one can reduce a 1H NMR spectrum to the structure [A] below. I speculated how a further test could be applied to this structure; back predicting its spectrum using just quantum mechanics. Overkill I know, but how well might the two match?
σ-π-Conjugation: seeking evidence by a survey of crystal structures.
February 3rd, 2013The electronic interaction between a single bond and an adjacent double bond is often called σ-π-conjugation (an older term for this is hyperconjugation), and the effect is often used to e.g. explain why more highly substituted carbocations are more stable than less substituted ones. This conjugation is more subtle in neutral molecules, but following my use of crystal structures to explore the so-called gauche effect (which originates from σ-σ-conjugation), I thought I would have a go here at seeing what the crystallographic evidence actually is for the σ-π-type.