I 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.
Archive for the ‘Interesting chemistry’ Category
A to-and-fro of electrons operating in s-cis esters.
Thursday, February 21st, 2013Linking numbers, and twist and writhe components for two extended porphyrins.
Sunday, 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.
Tuesday, 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.
Monday, 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.
Sunday, 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?
Friday, 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 …
σ-π-Conjugation: seeking evidence by a survey of crystal structures.
Sunday, 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.
How does one describe the wavefunction for the π-complex formed from PhNHOPh?
Friday, 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.
Aromaticity in the benzidine-like π-complex formed from PhNHOPh.
Saturday, 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?