Octopus publishing: dis-assembling the research article into eight components.

August 13th, 2021

In 2011, I suggested that the standard monolith that is the conventional scientific article could be broken down into two separate, but interlinked components, being the story or narrative of the article and the data on which the story is based. Later in 2018 the bibliography in the form of open citations were added as a distinct third component.[1] Here I discuss an approach that has taken this even further, breaking the article down into as many as eight components and described as “Octopus publishing” for obvious reasons. These are;

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References

  1. D. Shotton, "Funders should mandate open citations", Nature, vol. 553, pp. 129-129, 2018. http://dx.doi.org/10.1038/d41586-018-00104-7

Another very large anomeric effect – with a twist.

July 22nd, 2021

In the earlier post on the topic of anomeric effects, I identified a number of outliers associated with large differences in the lengths of two carbon-oxygen bonds sharing a common carbon atom.

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Dimerisation of cyclopropenylidene: what are the correct “curly arrows” for this process?

July 21st, 2021

In another post, a discussion arose about whether it might be possible to trap cyclopropenylidene to form a small molecule with a large dipole moment. Doing so assumes that cyclopropenylidene has a sufficiently long lifetime to so react, before it does so with itself to e.g. dimerise. That dimerisation has an energy profile shown below, with a free energy of activation of 14.4 kcal/mol, so a facile reaction that will indeed compete with reaction with Ph-I+-CC.

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Molecules with very large dipole moments: cyclopropenium acetylide

July 11th, 2021

Occasionally, someone comments about an old post here, asking a question. Such was the case here, when a question about the dipole moment of cyclopropenylidene arose. It turned out to be 3.5D, but this question sparked a thought about the related molecule below.

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Two record breakers for the anomeric effect; one real, the other not.

July 1st, 2021

The classic anomeric effect operates across a carbon atom attached to oxygens. One (of the two) lone pairs on the oxygen can donate into the σ* orbital of the C-O of the other oxygen (e.g. the red arrows) tending to weaken that bond whilst strengthening the donor oxygen C-O bond. Vice versa means e.g. the blue arrows weakening the other C-O bond. This effect tends to increase charge separation and the question then arises: how large can this effect get? To try to find out, we are going to do some crystal structure mining in this post!

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A closer look at that fourth bond in C2.

June 2nd, 2021

From the last few posts here, you might have noticed much discussion about how the element carbon might sustain a quadruple bond. The original post on this topic from some years ago showed the molecular orbitals of the species CN+, which included two bonding π-types and a low lying nodeless bonding σ-orbital, all with double occupancies and adding up to a triple bond. Discussing now C2 itself, there are two remaining orbitals for consideration which we will for the purpose here call the highest occupied σ-MO or HOσMO (Σu) and the lowest unoccupied σ-MO or LUσMO (Σg) and which are more mysterious.

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A reality-based suggestion for a molecule with a metal M⩸N quadruple bond.

May 13th, 2021

I noted in an earlier post the hypothesized example of (CO)3Fe⩸C[1] as exhibiting a carbon to iron quadruple bond and which might have precedent in known five-coordinate metal complexes where one of the ligands is a “carbide” or C ligand. I had previously mooted that the Fe⩸C combination might be replaceable by an isoelectronic Mn⩸N pair which could contain a quadruple bond to the nitrogen. An isoelectronic alternative to FeC could also be FeN+. Here I explore the possibility of realistic candidates for such bonded nitrogen.

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References

  1. A.J. Kalita, S.S. Rohman, C. Kashyap, S.S. Ullah, and A.K. Guha, "Transition metal carbon quadruple bond: viability through single electron transmutation", Physical Chemistry Chemical Physics, vol. 22, pp. 24178-24180, 2020. http://dx.doi.org/10.1039/d0cp03436c

A suggestion for a molecule with a M⩸C quadruple bond with trigonal metal coordination.

May 13th, 2021

The proposed identification of molecules with potential metal to carbon quadruple bonds, in which the metal exhibits trigonal bipyramidal coordination rather than the tetrahedral modes which have been proposed in the literature[1],[2],[3] leads on to asking whether simple trigonal coordination at the metal can also sustain this theme?

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References

  1. A.J. Kalita, S.S. Rohman, C. Kashyap, S.S. Ullah, and A.K. Guha, "Transition metal carbon quadruple bond: viability through single electron transmutation", Physical Chemistry Chemical Physics, vol. 22, pp. 24178-24180, 2020. http://dx.doi.org/10.1039/d0cp03436c
  2. A.J. Kalita, S.S. Rohman, C. Kashyap, S.S. Ullah, I. Baruah, L.J. Mazumder, P.P. Sahu, and A.K. Guha, "Is a transition metal–silicon quadruple bond viable?", Physical Chemistry Chemical Physics, vol. 23, pp. 9660-9662, 2021. http://dx.doi.org/10.1039/d1cp00598g
  3. L.F. Cheung, T. Chen, G.S. Kocheril, W. Chen, J. Czekner, and L. Wang, "Observation of Four-Fold Boron–Metal Bonds in RhB(BO–) and RhB", The Journal of Physical Chemistry Letters, vol. 11, pp. 659-663, 2020. http://dx.doi.org/10.1021/acs.jpclett.9b03484

What does a double σ-bond along a bond axis look like?

May 10th, 2021

Introductory chemistry will tell us that a triple bond between say two carbon atoms comprises just one bond of σ-axial symmetry and two of π-symmetry. Increasingly mentioned nowadays is the possibility of a quadruple bond between carbon and either itself or a transition metal, as discussed in the previous post. Such a bond comprises TWO bonds of σ-axial symmetry. Since most people are unfamiliar with such double bonds and in particular with how that second σ-bond sits with the first, I thought it would be interesting to show such an orbital. This one is a localised orbital 41, selected from the previous post for the molecule (PH3)2(CN)2Mo⩸C. Read the rest of this entry »

Two new reality-based suggestions for molecules with a metal M⩸C quadruple bond.

May 8th, 2021

Following from much discussion over the last decade about the nature of C2, a diatomic molecule which some have suggested sustains a quadruple bond between the two carbon atoms, new ideas are now appearing for molecules in which such a bond may also exist between carbon and a transition metal atom. A suggested, albeit hypothetical example was C⩸Fe(CO)3[1]. Iron has a [Ar].3d6.4s2 electronic configuration and if we ionise to balance a C4- ligand, the iron becomes formally FeVI or [Ar].3d4. By adding 14 electrons deriving from the seven “bonds” to the 3d4, including a quadruple count from carbon, the Fe formally completes its 18-electron valence shell, as also found in e.g. Ferrocene.

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References

  1. A.J. Kalita, S.S. Rohman, C. Kashyap, S.S. Ullah, and A.K. Guha, "Transition metal carbon quadruple bond: viability through single electron transmutation", Physical Chemistry Chemical Physics, vol. 22, pp. 24178-24180, 2020. http://dx.doi.org/10.1039/d0cp03436c