Do you fancy a story going from simplicity to complexity, if not absurdity, in three easy steps? Read on! The following problem appears in one of our (past) examination questions in introductory organic chemistry. From relatively mundane beginnings, one can rapidly find oneself in very unexpected territory. How would one make 3-nitrobenzonitrile?
A conjugated, (apparently) aromatic molecular trefoil might be expected to have some unusual, if not extreme properties. Here some of these are explored. The first is the vibrational spectrum. With 144 atoms for this molecule, it has 426 vibrational modes, but one is highlighted below. This is the mode that moves the atoms in accord with the Kekulé resonance. If real, this mode resists such alternation.
Since I have gotten into the habit of quoting some of my posts in other contexts, I have started to also archive them using WebCite. One can quote the resulting archive as: Rzepa, Henry. Quintuple bonds. 2010-04-18. URL:http://www.ch.ic.ac.uk/rzepa/blog/?p=1722. Accessed: 2010-04-18. (Archived by WebCite ® at http://www.webcitation.org/5p5BtuzSH) There is one issue though.
Metadata is something that goes on behind the scenes and is rarely of concern to either author or readers of scientific articles. Here I tell a story where it has rather greater exposure. For journals in science and chemistry, each article published has a corresponding metadata record, associated with the persistent identifier of the article and known to most as its DOI.
I should start by saying that the server on which this blog is posted was set up in June 1993. Although the physical object has been replaced a few times, and had been “virtualised” about 15 years ago, a small number of the underlying software base components may well date way back, perhaps even to 1993.
Having shown that carbon as a carbene centre, C : can act as a hydrogen bond acceptor, as seen from a search of crystal structures, I began to wonder if there is any chance that carbon as a radical centre, C• could do so as well. Definitely a subversive thought, since radical centres are supposed to abstract hydrogens rather than to hydrogen bond to them.
The conventional procedures for reporting analysis or new results in science is to compose an “article”, augment that perhaps with “supporting information” or “SI”, submit to a journal which undertakes peer review, with revision as necessary for acceptance and finally publication. If errors in the original are later identified, a separate corrigendum can be submitted to the same journal, although this is relatively rare.
Here is another molecule of the year, on a topic close to my heart, the catenane systems 1 and the trefoil knot 2 [cite]10.1126/science.aav5021[/cite] Such topology is closely inter-twinned with three dimensions (literally) and I always find that the flat pages of a journal are simply insufficient to do them justice. So I set about finding the 3D coordinates.
In the previous post, I noted the crystallographic detection of an unusually short non-bonded H…H contact of ~1.5Å, some 0.9Å shorter than twice the van der Waals radius of hydrogen (1.2Å, although some sources quote 1.1Å which would make the contraction ~0.7Å). This was attributed to dispersion attractions accumulating in the rest of the molecule.
The molecules below were discussed in the previous post as examples of highly polar but formally neutral molecules, a property induced by aromatisation of up to three rings. Since e.g. compound 3 is known only in its protonated phenolic form, here I take a look at the basicity of the oxygen in these systems to see if deprotonation of the ionic phenol form to the neutral polar form is viable.