A PID or persistent identifier has been in common use in scientific publishing for around 20 years now. It was introduced as a DOI (Digital Object Identifier), and the digital object in this case was the journal article. From 2000 onwards, DOIs started appearing for most journal articles, journals having obtained them from a registration agency, CrossRef. This is a not-for-profit organisation set up by a publishers association for the purpose. Most readers of journal articles started to use this DOI as an easier way of navigating through invariably different and sometimes confusing metaphors set up by any given journal to navigate through its issues. Readers slowly learnt to prepend the URL http://dx.doi.org/ to the DOI to “resolve” it directly to what is known as the “landing page” of the article. More recently, the prefix recommendation has changed to the slightly shorter https://doi.org/ form. Few readers are aware however that the DOI can serve a much more interesting purpose than just taking you to the article landing page. This post will explore a few of these extras.
The Persistent Identifier ecosystem expands – to instruments!
March 21st, 2020The singlet and open shell higher-spin states of [4], [6] and [8]-annulenes and their Kekulé vibrational modes
March 11th, 2020In 2001, Shaik and co-workers published the first of several famous review articles on the topic A Different Story of π-Delocalization. The Distortivity of π-Electrons and Its Chemical Manifestations[1]. The main premise was that the delocalized π-electronic component of benzene is unstable toward a localizing distortion and is at the same time stabilized by resonance relative to a localized reference structure. Put more simply, the specific case of benzene has six-fold symmetry because of the twelve C-C σ-electrons and not the six π-electrons. In 2009, I commented here on this concept, via a calculation of the quintet state of benzene in which two of the six π-electrons are excited from bonding into anti-bonding π-orbitals, thus reducing the total formal π-bond orders around the ring from three to one. I focused on a particular vibrational normal mode, which is usefully referred to as the Kekulé mode, since it lengthens three bonds in benzene whilst shortening the other three. In this case the stretching wavenumber increased by ~207 cm-1 when the total π-bond order of benzene was reduced from three to one by spin excitation. In other words, each C-C bond gets longer when the π-electrons are excited, but the C-C bond itself gets stronger (in terms at least of the Kekulé mode).† This behaviour is called a violation of Badger’s rule[2] for the relationship between the length of a bond and its stretching force constant.
References
- S. Shaik, A. Shurki, D. Danovich, and P.C. Hiberty, "A Different Story of π-DelocalizationThe Distortivity of π-Electrons and Its Chemical Manifestations", Chemical Reviews, vol. 101, pp. 1501-1540, 2001. https://doi.org/10.1021/cr990363l
- R.M. Badger, "A Relation Between Internuclear Distances and Bond Force Constants", The Journal of Chemical Physics, vol. 2, pp. 128-131, 1934. https://doi.org/10.1063/1.1749433
Encouraging Submission of FAIR Data at the Journal of Organic Chemistry and Organic Letters
February 14th, 2020In a welcome move, one of the American chemical society journals has published an encouragement to submit what is called FAIR data to the journal.[1]. A reminder that FAIR data is data that can be Found (F), Accessed (A), Interoperated(I) and Re-used( R). I thought I might try to explore this new tool here.
References
- A.M. Hunter, E.M. Carreira, and S.J. Miller, "Encouraging Submission of FAIR Data at <i>The Journal of Organic Chemistry</i> and <i>Organic Letters</i>", Organic Letters, vol. 22, pp. 1231-1232, 2020. https://doi.org/10.1021/acs.orglett.0c00383
Molecules of the year 2019: Hexagonal planar crystal structures.
January 23rd, 2020Here is another selection from the Molecules-of-the-Year shortlist published by C&E News, in which hexagonal planar transition metal coordination is identified. This was a mode of metal coordination first mooted more than 100 years ago,[1] but with the first examples only being discovered recently. The C&E News example comprises a central palladium atom surrounded by three hydride and three magnesium atoms, all seven atoms being in the same plane.
References
- M. Garçon, C. Bakewell, G.A. Sackman, A.J.P. White, R.I. Cooper, A.J. Edwards, and M.R. Crimmin, "A hexagonal planar transition-metal complex", Nature, vol. 574, pp. 390-393, 2019. https://doi.org/10.1038/s41586-019-1616-2
Comment on “Resolving the Quadruple Bonding Conundrum in C2 Using Insights Derived from Excited State Potential Energy Surfaces”: The 7Σ heptet excited states for related molecules.
January 2nd, 2020I noted in an earlier blog, a potential (if difficult) experimental test of the properties of the singlet state of dicarbon, C2. Now, just a few days ago, a ChemRxiv article has been published suggesting another (probably much more realistic) test.[1] This looks at the so-called 7Σ open shell state of the molecule where three electrons from one σ and two π orbitals are excited into the corresponding σ* and π* unoccupied orbitals. The argument is presented that these states are not dissociative, showing a deep minimum and hence a latent quadruple bonding nature. They also note that the isoelectronic BN molecule IS dissociative.† Thus to quote: “Hence, the proof of existence of a minimum in the 7Σu+ for C2 and the absence of such a minimum in the equivalent case for BN is likely to corroborate our findings on quadruple bonding in these two cases.“
References
- I. Bhattacharjee, D. Ghosh, and A. Paul, "Resolving the Quadruple Bonding Conundrum in C2 Using Insights Derived from Excited State Potential Energy Surfaces: A Molecular Orbital Perspective", 2019. https://doi.org/10.26434/chemrxiv.11446224.v1
Can a carbon radical act as a hydrogen bond acceptor?
December 28th, 2019Having 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.
Carbon as a hydrogen bond acceptor: can dicarbon (C2) act in this manner?
December 27th, 2019In the previous post, I showed that carbon can act as a hydrogen bond acceptor (of a proton) to form strong hydrogen bond complexes. Which brings me to a conceptual connection: can singlet dicarbon form such a hydrogen bond?
Hydrogen bonds: carbon as an acceptor rather than as a donor?
December 23rd, 2019A hydrogen bond donor is considered as an electronegative element carrying a hydrogen that is accepted by an atom carrying a lone pair of electrons, as in X:…H-Y where X: is the acceptor and H-Y the donor. Wikipedia asserts that carbon can act as a donor, as we saw in the post on the incredible chloride cage, where six Cl:…H-C interactions trapped the chloride ion inside the cage. This led me to ask how many examples are there of carbon as an acceptor rather than as a donor?
Molecules of the year – 2019: twisty tetracene.
December 22nd, 2019All of the molecules in this year’s C&EN list are fascinating in their very different ways. Here I take a look at the twisty tetracene (dodecaphenyltetracene) which is indeed very very twisty.[1]
References
- Y. Xiao, J.T. Mague, R.H. Schmehl, F.M. Haque, and R.A. Pascal, "Dodecaphenyltetracene", Angewandte Chemie International Edition, vol. 58, pp. 2831-2833, 2019. https://doi.org/10.1002/anie.201812418
L-Malic acid: An exercise in conformational analysis impacting upon optical rotatory dispersion (ORD).
December 20th, 2019My momentum of describing early attempts to use optical rotation to correlate absolute configuration of small molecules such as glyceraldehyde and lactic acid with their optical rotations has carried me to L-Malic acid (below labelled as (S)-Malic acid).