Ten years on: Jmol and WordPress.

May 16th, 2018

Ten years are a long time when it comes to (recent) technologies. The first post on this blog was on the topic of how to present chemistry with three intact dimensions. I had in mind molecular models, molecular isosurfaces and molecular vibrations (arguably a further dimension). Here I reflect on how ten years of progress in technology has required changes and the challenge of how any necessary changes might be kept “under the hood” of this blog.

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Examples please of FAIR (data); good and bad.

May 6th, 2018

The site fairsharing.org is a repository of information about FAIR (Findable, Accessible, Interoperable and Reusable) objects such as research data.

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Aromaticity-induced basicity.

April 18th, 2018

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.

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A record polarity for a neutral compound?

April 13th, 2018

In several posts a year or so ago I considered various suggestions for the most polar neutral molecules, as measured by the dipole moment. A record had been claimed[1] for a synthesized molecule of ~14.1±0.7D. I pushed this to a calculated 21.7D for an admittedly hypothetical and unsynthesized molecule. Here I propose a new family of compounds which have the potential to extend the dipole moment for a formally neutral molecule up still further.

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References

  1. J. Wudarczyk, G. Papamokos, V. Margaritis, D. Schollmeyer, F. Hinkel, M. Baumgarten, G. Floudas, and K. Müllen, "Hexasubstituted Benzenes with Ultrastrong Dipole Moments", Angewandte Chemie International Edition, vol. 55, pp. 3220-3223, 2016. http://dx.doi.org/10.1002/anie.201508249

The dark satanic mills (of the industrial revolution?)

March 18th, 2018

Around the time of the 2012 olympic games, the main site for which was Stratford in east London, I heard a fascinating talk about the “remediation” of the site from the pollution caused by its industrial chemical heritage. Here I visit another, arguably much more famous and indeed older industrial site.

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Never mind main group “hypervalency”, what about transition metal “hypervalency”?

March 18th, 2018

I have posted often on the chemical phenomenon known as hypervalency, being careful to state that as defined it applies just to “octet excess” in main group elements. But what about the next valence shell, occurring in transition metals and known as the “18-electron rule”? You rarely hear the term hypervalency being applied to such molecules, defined presumably by the 18-electron valence shell count being exceeded. So the following molecule (drawn in three possible valence bond representations) first made in 1992 intrigues.[1]

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References

  1. R. Ahlrichs, D. Fenske, H. Oesen, and U. Schneider, "Synthesis and Structure of[Ni(PtBu6)] and[Ni5(PtBu)6(CO)5] and Calculations on the Electronic Structure of[Ni(PtBu)6] and(PR)6, R=tBu,Me", Angewandte Chemie International Edition in English, vol. 31, pp. 323-326, 1992. http://dx.doi.org/10.1002/anie.199203231

How FAIR are the data associated with the 2017 Molecules-of-the-Year?

March 7th, 2018

C&EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is.

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What are the highest bond indices for main group and transition group elements?

March 4th, 2018

A bond index (BI) approximately measures the totals of the bond orders at any given atom in a molecule. Here I ponder what the maximum values might be for elements with filled valence shells.

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Hypervalent or not? A fluxional triselenide.

February 24th, 2018

Another post inspired by a comment on an earlier one; I had been discussing compounds of the type I.In (n=4,6) as possible candidates for hypervalency. The comment suggests the below as a similar analogue, deriving from observations made in 1989.[1]

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References

  1. Y. Mazaki, and K. Kobayashi, "Structure and intramolecular dynamics of bis(diisobutylselenocarbamoyl) triselenide as identified in solution by the 77Se-NMR spectroscopy", Tetrahedron Letters, vol. 30, pp. 2813-2816, 1989. http://dx.doi.org/10.1016/S0040-4039(00)99132-9

Is (hν)3 an allotrope of light?

February 23rd, 2018

A little while ago I pondered allotropic bromine, or Br(Br)3. But this is a far wackier report[1] of a molecule of light.

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References

  1. Q. Liang, A.V. Venkatramani, S.H. Cantu, T.L. Nicholson, M.J. Gullans, A.V. Gorshkov, J.D. Thompson, C. Chin, M.D. Lukin, and V. Vuletić, "Observation of three-photon bound states in a quantum nonlinear medium", Science, vol. 359, pp. 783-786, 2018. http://dx.doi.org/10.1126/science.aao7293