Archive for the ‘Interesting chemistry’ Category

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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Molecules of the year – 2019: twisty tetracene.

Sunday, December 22nd, 2019

All 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]

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References

  1. 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. http://dx.doi.org/10.1002/anie.201812418

Molecules of the year – 2019: Topological molecular nanocarbons – All-benzene catenane and trefoil knot.

Sunday, December 15th, 2019

Here is another molecule of the year, on a topic close to my heart, the catenane systems 1 and the trefoil knot 2[1] 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.

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References

  1. Y. Segawa, M. Kuwayama, Y. Hijikata, M. Fushimi, T. Nishihara, J. Pirillo, J. Shirasaki, N. Kubota, and K. Itami, "Topological molecular nanocarbons: All-benzene catenane and trefoil knot", Science, vol. 365, pp. 272-276, 2019. http://dx.doi.org/10.1126/science.aav5021

Molecules of the year – 2019: the incredible chloride cage.

Friday, December 13th, 2019

Each year, C&E News runs a poll for their “Molecule of the year“. I occasionally comment with some aspect of one of the molecules that catches my eye (I have already written about cyclo[18]carbon, another in the list). Here, it is the Incredible chloride cage, a cryptand-like container with an attomolar (1017 M-1) affinity for a chloride anion.[1] The essence of the binding is six short CH…Cl and one slightly longer interactions to the same chloride (DOI: 10.5517/ccdc.csd.cc1ngqrl) and one further hydrogen bond to a water molecule; eight coordinated chloride anion!

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References

Sign inversions in optical rotation as a function of wavelength (ORD spectra)

Monday, December 9th, 2019

I have been discussing some historical aspects of the absolute configuration of molecules and how it was connected to their optical rotations. The nomenclature for certain types of molecules such as sugars and less commonly amino acids includes the notation (+) to indicate that the specific optical rotation of the molecule has a positive (rather than a negative) value. What is rarely mentioned is the implicit wavelength at which the rotation is measured. Historically polarimeters operated at the so-called sodium Fraunhofer D-line (588.995nm, hence the name [α]D) and only much more recently at the mercury e-line (546.073nm). The former was used for uncoloured organic molecules, since it was realised early on that colour and optical rotation did not mix well. Here I take a closer look at this aspect by constructing the hypothetical molecule shown below.

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