A Theoretical Method for Distinguishing X‐H Bond Activation Mechanisms.

July 25th, 2018
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Consider the four reactions. The first two are taught in introductory organic chemistry as (a) a proton transfer, often abbreviated PT, from X to B (a base) and (b) a hydride transfer from X to A (an acid). The third example is taught as a hydrogen atom transfer or HAT from X to (in this example) O. Recently an article has appeared[1] citing an example of a fourth fundamental type (d), which is given the acronym cPCET which I will expand later. Here I explore this last type a bit further, in the context that X-H bond activations are currently a very active area of research.

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References

  1. J.E.M.N. Klein, and G. Knizia, "cPCET versus HAT: A Direct Theoretical Method for Distinguishing X-H Bond-Activation Mechanisms", Angewandte Chemie International Edition, vol. 57, pp. 11913-11917, 2018. http://dx.doi.org/10.1002/anie.201805511

FAIR Data in Amsterdam – FAIR data points.

July 18th, 2018
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FAIR is one of those acronyms that spreads rapidly, acquires a life of its own and can mean many things to different groups. A two-day event has just been held in Amsterdam to bring some of those groups from the chemical sciences together to better understand FAIR. Here I note a few items that caught my attention.

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Chemistry (and music) in the Park.

July 12th, 2018
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This last month, as a follow-up to the preceding post on the colour of flowers, I have been moonlighting by blogging elsewhere. Do go visit my “guerrilla blog” at perivalepark.london. Part of this project involves visiting two “physic or botanic” gardens, which originate from early 17th century explorations of herbs and other botanicals as medicines. Both are very old and their chemistry is indeed fascinating; more of which later.

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Why do flowers such as roses, peonies, dahlias, delphiniums (etc), exhibit so many shades of colours?

June 18th, 2018
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It was about a year ago that I came across a profusion of colour in my local Park. Although colour in fact was the topic that sparked my interest in chemistry many years ago (the fantastic reds produced by diazocoupling reactions), I had never really tracked down the origin of colours in many flowers. It is of course a vast field. Here I take a look at just one class of molecule responsible for many flower colours, anthocyanidin, this being the sugar-free counterpart of the anthocyanins found in nature.

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Ten years on: Jmol and WordPress.

May 16th, 2018
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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
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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
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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
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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
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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
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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