ORCID identifiers galore!

April 21st, 2015
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Egon has reminded us that adoption of ORCID (Open researcher and collaborator ID) is gaining apace. It is a mechanism to disambiguate (a Wikipedia term!) contributions in the researcher community and to also remove much of the anonymity (where that is undesirable) that often lurks in social media sites.

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A new way of exploring the directing influence of (electron donating) substituents on benzene.

April 17th, 2015
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The knowledge that substituents on a benzene ring direct an electrophile engaged in a ring substitution reaction according to whether they withdraw or donate electrons is very old.[1] Introductory organic chemistry tells us that electron donating substituents promote the ortho and para positions over the meta. Here I try to recover some of this information by searching crystal structures.

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References

  1. H.E. Armstrong, "XXVIII.?An explanation of the laws which govern substitution in the case of benzenoid compounds", Journal of the Chemical Society, Transactions, vol. 51, pp. 258, 1887. http://dx.doi.org/10.1039/CT8875100258

The mechanism of borohydride reductions. Part 1: ethanal.

April 12th, 2015
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Sodium borohydride is the tamer cousin of lithium aluminium hydride (LAH). It is used in aqueous solution to e.g. reduce aldehydes and ketones, but it leaves acids, amides and esters alone. Here I start an exploration of why it is such a different reducing agent.
BH4

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A better model for the mechanism of Lithal (LAH) reduction of cinnamaldehyde?

April 10th, 2015
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Previously on this blog: modelling the reduction of cinnamaldehyde using one molecule of lithal shows easy reduction of the carbonyl but a high barrier at the next stage, the reduction of the double bond. Here is a quantum energetic exploration of what might happen when a second LAH is added to the brew (the usual ωB97XD/6-311+G(d,p)/SCRF=diethyl ether).

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Goldilocks Data.

April 8th, 2015
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Last August, I wrote about data galore, the archival of data for 133,885 (134 kilo) molecules into a repository, together with an associated data descriptor[1] published in the new journal Scientific Data. Since six months is a long time in the rapidly evolving field of RDM, or research data management, I offer an update in the form of some new observations.

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References

  1. R. Ramakrishnan, P.O. Dral, M. Rupp, and O.A. von Lilienfeld, "Quantum chemistry structures and properties of 134 kilo molecules", Scientific Data, vol. 1, 2014. http://dx.doi.org/10.1038/sdata.2014.22

Mechanism of the Lithal (LAH) reduction of cinnamaldehyde.

April 1st, 2015
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The reduction of cinnamaldehyde by lithium aluminium hydride (LAH) was reported in a classic series of experiments[1],[2],[3] dating from 1947-8. The reaction was first introduced into the organic chemistry laboratories here at Imperial College decades ago, vanished for a short period, and has recently been reintroduced again. The experiment is really simple in concept; add LAH to cinnamaldehyde and you get just reduction of the carbonyl group; invert the order of addition and you additionally get reduction of the double bond. Here I investigate the mechanism of these reductions using computation (ωB97XD/6-311+G(d,p)/SCRF=diethyl ether).

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References

  1. R.F. Nystrom, and W.G. Brown, "Reduction of Organic Compounds by Lithium Aluminum Hydride. I. Aldehydes, Ketones, Esters, Acid Chlorides and Acid Anhydrides", J. Am. Chem. Soc., vol. 69, pp. 1197-1199, 1947. http://dx.doi.org/10.1021/ja01197a060
  2. R.F. Nystrom, and W.G. Brown, "Reduction of Organic Compounds by Lithium Aluminum Hydride. II. Carboxylic Acids", J. Am. Chem. Soc., vol. 69, pp. 2548-2549, 1947. http://dx.doi.org/10.1021/ja01202a082
  3. F.A. Hochstein, and W.G. Brown, "Addition of Lithium Aluminum Hydride to Double Bonds", J. Am. Chem. Soc., vol. 70, pp. 3484-3486, 1948. http://dx.doi.org/10.1021/ja01190a082

Ionizing yet more ultra-strong acids with water molecules.

March 20th, 2015
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This might be seen as cranking a handle by producing yet more examples of acids ionised by a small number of water molecules. I justify it (probably only to myself) as an exercise in how a scientist might approach a problem, and how it linearly develops with time, not necessarily in the directions first envisaged. A conventional scientific narrative published in a conventional journal tells the story often with the benefit of hindsight, but rarely how the project actually unfolded chronologically. So by devoting 7 posts to this, you can judge for yourself how my thoughts might have developed (and I am prepared to acknowledge this may only serve to show my ignorance).

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A 5-high straight flush of water-ionised acids?

March 17th, 2015
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I do not play poker, and so I had to look up a 5-4-3-2-1(A), which Wikipedia informs me is a 5-high straight flush, also apparently known as a steel wheel. In previous posts  I have suggested acids which can be ionised by (probably) 5, 4, 3 or  1 discrete water molecules in the gas phase; now to try to track down  a candidate for ionisation by the required two water molecules to form that straight flush.

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Ionizing ultra-strong acids with water molecules.

March 15th, 2015
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My previous posts have covered the ionization by a small number of discrete water molecules of the series of halogen acids, ranging from HI (the strongest, pKa -10) via HF (weaker, pKa 3.1) to the pseudo-halogen HCN (the weakest, pKa 9.2). Here I try out some even stronger acids to see what the least number of water molecule needed to ionize these might be.

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How many water molecules does it take to ionise HCN/HNC? An NCI exploration.

March 2nd, 2015
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HCN is a weak acid (pKa +9.2, weaker than e.g. HF), although it does have an isomer, isocyanic acid or HNC (pka < +9.2 ?) which is simultaneously stronger and less stable. I conclude my halide acid series by investigating how many water molecules (in gas phase clusters) are required for ionisation of this “pseudo-halogen” acid.

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