Archive for the ‘Interesting chemistry’ Category

Fascinating stereoelectronic control in Metaldehyde and Chloral.

Tuesday, June 9th, 2020

Metaldehyde is an insecticide used to control slugs. When we unsuccessfully tried to get some recently, I discovered it is now deprecated in the UK. So my immediate reaction was to look up its structure to see if that cast any light (below, R=CH3, shown as one stereoisomer).

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The strongest bond in the universe: revisited ten years on.

Saturday, May 23rd, 2020

I occasionally notice that posts that first appeared here many years ago suddenly attract attention. Thus this post, entitled The strongest bond in the universe, from ten years back, has suddently become the most popular, going from an average of 0-2 hits per day to 92 in a single day on May 22nd (most views appear to originate from India). I can only presume that a university there has set some course work on this topic and Google has helped some of the students identify my post. Well, re-reading something you wrote ten years ago can be unsettling. Are the conclusions still sound? Would I establish my claim the same way now? After all, one picks up a little more experience in ten years. So here is my revisitation.

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Discussion of (the) Room-temperature chemical synthesis of dicarbon – open and transparent science.

Wednesday, May 6th, 2020

A little more than a year ago, a ChemRxiv pre-print appeared bearing the title referenced in this post,[1] which immediately piqued my curiosity. The report presented persuasive evidence, in the form of trapping experiments, that dicarbon or C2 had been formed by the following chemical synthesis. Here I describe some of what happened next, since it perhaps gives some insight into the processes of bringing a scientific result into the open.

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References

  1. K. Miyamoto, S. Narita, Y. Masumoto, T. Hashishin, M. Kimura, M. Ochiai, and M. Uchiyama, "Room-Temperature Chemical Synthesis of C2", 2019. http://dx.doi.org/10.26434/chemrxiv.8009633.v1

A molecular sponge for hydrogen storage- the future for road transport?

Sunday, April 19th, 2020

In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus “NU-1501-Al” can absorb 14 weight% of hydrogen. To power a low-polluting car with a 500 km range, about 4-5 kg of hydrogen gas would be need to be stored and released safely. The molecule is of interest since it opens a systematic strategy of synthetically driven optimisation towards a viable ultra-porous storage material,[1] much like a lead drug compound can be optimised.

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References

  1. Z. Chen, P. Li, R. Anderson, X. Wang, X. Zhang, L. Robison, L.R. Redfern, S. Moribe, T. Islamoglu, D.A. Gómez-Gualdrón, T. Yildirim, J.F. Stoddart, and O.K. Farha, "Balancing volumetric and gravimetric uptake in highly porous materials for clean energy", Science, vol. 368, pp. 297-303, 2020. http://dx.doi.org/10.1126/science.aaz8881

The singlet and open shell higher-spin states of [4], [6] and [8]-annulenes and their Kekulé vibrational modes

Wednesday, March 11th, 2020

In 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. 

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References

  1. 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. http://dx.doi.org/10.1021/cr990363l
  2. R.M. Badger, "A Relation Between Internuclear Distances and Bond Force Constants", The Journal of Chemical Physics, vol. 2, pp. 128-131, 1934. http://dx.doi.org/10.1063/1.1749433

Encouraging Submission of FAIR Data at the Journal of Organic Chemistry and Organic Letters

Friday, February 14th, 2020

In 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.

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References

  1. A.M. Hunter, E.M. Carreira, and S.J. Miller, "Encouraging Submission of FAIR Data at The Journal of Organic Chemistry and Organic Letters", Organic Letters, vol. 22, pp. 1231-1232, 2020. http://dx.doi.org/10.1021/acs.orglett.0c00383

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.

Thursday, January 2nd, 2020

I 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.

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References

  1. 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. http://dx.doi.org/10.26434/chemrxiv.11446224.v1

Can a carbon radical act as a hydrogen bond acceptor?

Saturday, December 28th, 2019

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.

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Carbon as a hydrogen bond acceptor: can dicarbon (C2) act in this manner?

Friday, December 27th, 2019

In 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? 

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Hydrogen bonds: carbon as an acceptor rather than as a donor?

Monday, December 23rd, 2019

A 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?

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