This 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. Ramachandran plots.
February 11th, 2013The 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.
Secrets of a university tutor: unravelling a mechanism using spectroscopy.
January 31st, 2013It is always rewarding when one comes across a problem in chemistry that can be solved using a continuous stream of rules and logical inferences from them. The example below[cite]10.1039/P19930000299[/cite] is one I have been using as a tutor in organic chemistry for a few years now, and I share it here. It takes around 50 minutes to unravel with students.
How does one describe the wavefunction for the π-complex formed from PhNHOPh?
January 25th, 2013Although have dealt with the π-complex formed by protonation of PhNHOPh in several posts, there was one aspect that I had not really answered; what is the most appropriate description of its electronic nature? Here I do not so much provide an answer, as try to show how difficult getting an accurate answer might be.
The demographics of a blog readership.
January 20th, 2013With metrics in science publishing controversial to say the least, I pondered whether to write about the impact/influence a science-based blog might have (never mind whether it constitutes any measure of esteem). These are all terms that feature large when an (academic) organisation undertakes a survey of its researchers’ effectiveness.‡ WordPress (the organisation that provides the software used for this blog) recently enhanced the stats it offers for its users, and one of these caught my eye.
Aromaticity in the benzidine-like π-complex formed from PhNHOPh.
January 19th, 2013The transient π-complex formed during the “[5,5]” sigmatropic rearrangement of protonated N,O-diphenyl hydroxylamine can be (formally) represented as below, namely the interaction of a six-π-electron aromatic ring (the phenoxide anion 2) with a four-π-electron phenyl dication-anion pair 1. Can one analyse this interaction in terms of aromaticity?