March 24th, 2019
There is a predilection amongst chemists for collecting records; one common theme is the length of particular bonds, either the shortest or the longest. A particularly baffling type of bond is that between the very electronegative F atom and an acid hydrogen atom such as that in OH. Thus short C-N…HO hydrogen bonds are extremely common, as are C-O…HO.‡ But F atoms in C-F bonds are largely thought to be inert to hydrogen bonding, as indicated by the use of fluorine in many pharmaceuticals as inert isosteres.[1] Here I do an up-to-date search of the CSD crystal structure database, which is now on the verge of accumulating 1 million entries, to see if any strong C-F…HO hydrogen bonding may have been recently discovered.
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References
- S. Purser, P.R. Moore, S. Swallow, and V. Gouverneur, "Fluorine in medicinal chemistry", Chem. Soc. Rev., vol. 37, pp. 320-330, 2008. https://doi.org/10.1039/b610213c
Tags: Chemical bond, chemical bonding, Chemical elements, Chemistry, Fluorine, Hydrogen, Hydrogen bond, Intermolecular forces, Natural sciences, perturbation energy, pharmaceuticals, Physical sciences, Refrigerants, search parameters, search query, Supramolecular chemistry
Posted in crystal_structure_mining | No Comments »
February 18th, 2019
Students learning organic chemistry are often asked in examinations and tutorials to devise the mechanisms (as represented by curly arrows) for the core corpus of important reactions, with the purpose of learning skills that allow them to go on to improvise mechanisms for new reactions. A common question asked by students is how should such mechanisms be presented in an exam in order to gain full credit? Alternatively, is there a single correct mechanism for any given reaction? To which the lecturer or tutor will often respond that any reasonable mechanism will receive such credit. The implication is that a mechanism is “reasonable” if it “follows the rules”. The rules are rarely declared fully, but seem to be part of the absorbed but often mysterious skill acquired in learning the subject. These rules also include those governing how the curly arrows should be drawn.† Here I explore this topic using the Graham reaction.[1]‡
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References
- W.H. Graham, "The Halogenation of Amidines. I. Synthesis of 3-Halo- and Other Negatively Substituted Diazirines<sup>1</sup>", Journal of the American Chemical Society, vol. 87, pp. 4396-4397, 1965. https://doi.org/10.1021/ja00947a040
Tags: /RT, activation energy, activation free energy, animation, arrow pushing, arrow-head, cellular telephone, Chemical kinetics, chemical reaction, Chemistry, computed energy, Ed Smith, energy, energy maximum, energy minima, energy plot, energy profile, energy surface, free energy, lecturer, mechanism, Natural sciences, Organic chemistry, overall reaction energy, Physical sciences, Reaction rate constant, Resonance, Transition state, Transition state theory, tutor, Tutorial
Posted in Curly arrows, Interesting chemistry | No Comments »
February 16th, 2019
Tags: Aaron Swartz, Academic publishing, API, Business intelligence, CrossRef, data, Data management, Elsevier, favourite publisher, Identifiers, Information, Information science, Knowledge, Knowledge representation, metadata, mining, ORCiD, PDF, Pre-exposure prophylaxis, Publishing, Publishing Requirements for Industry Standard Metadata, Records management, Research Object, Scholarly communication, Scientific literature, search engine, social media, Technical communication, Technology/Internet, text mining, Written communication, XML
Posted in Interesting chemistry | 1 Comment »
January 22nd, 2019
Tags: Biblical manuscripts, Book design, Book of Kells, Books, City: Dublin, County Meath, Dublin, Hospitality/Recreation, Illuminated manuscript, Kells, Manuscripts, Trinity College, Trinity College Dublin, Trinity College Library, Trinity College Library Dublin, Western art, Woad plant
Posted in Interesting chemistry | No Comments »
January 13th, 2019
Tags: Benzoic acid, Chemical kinetics, chemical reaction, chemical reactivity, chemist, Chemistry, Electrophilic aromatic substitution, energy point, Equations, Equilibrium chemistry, Equilibrium constant, free energy overall route, Hammett equation, Linear free energy relationships, Natural sciences, Organic chemistry, Physical organic chemistry, Physical sciences, Reactivity
Posted in Chemical IT, Interesting chemistry, reaction mechanism | No Comments »
January 3rd, 2019
There is emerging interest in cyclic conjugated molecules that happen to have triplet spin states and which might be expected to follow a 4n rule for aromaticity.[1] The simplest such system would be the triplet state of cyclobutadiene, for which a non or anti-aromatic singlet state is always found to be lower in energy. Here I explore some crystal structures containing this motif for possible insights.
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References
- A. Kostenko, B. Tumanskii, Y. Kobayashi, M. Nakamoto, A. Sekiguchi, and Y. Apeloig, "Spectroscopic Observation of the Triplet Diradical State of a Cyclobutadiene", Angewandte Chemie International Edition, vol. 56, pp. 10183-10187, 2017. https://doi.org/10.1002/anie.201705228
Tags: antiaromaticity, aromaticity, Baird's rule, Conjugated system, crystal structure search, energy, Hückel's rule, Nature, Physical organic chemistry, Physical sciences, search query, Triplet state
Posted in Interesting chemistry | No Comments »
December 29th, 2018
The traditional structure of the research article has been honed and perfected for over 350 years by its custodians, the publishers of scientific journals. Nowadays, for some journals at least, it might be viewed as much as a profit centre as the perfected mechanism for scientific communication. Here I take a look at the components of such articles to try to envisage its future, with the focus on molecules and chemistry.
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Tags: Academic publishing, Acrobat, Articles, chemical discoveries, data, Data management, ELN, Information, Molecules, Narrative, PDF, Publishing, Research, Scholarly communication, Science, Scientific Journal, Scientific method, Technical communication, Technology/Internet, Web browser
Posted in Chemical IT | No Comments »
December 21st, 2018
Five years back, I speculated about the mechanism of the epoxidation of ethene by a peracid, concluding that kinetic isotope effects provided interesting evidence that this mechanism is highly asynchronous and involves a so-called “hidden intermediate”. Here I revisit this reaction in which a small change is applied to the atoms involved.
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Tags: Chemical kinetics, chemical reaction, Chemistry, Deuterium, Isotope effect, Kinetic isotope effect, Natural sciences, Organic chemistry, overall activation energy, pericyclic reaction, Physical organic chemistry, Physical sciences, potential energy surface, Rearrangement reactions
Posted in Interesting chemistry | 5 Comments »
November 4th, 2018
For perhaps ten years now, the future of scientific publishing has been hotly debated. The traditional models are often thought to be badly broken, although convergence to a consensus of what a better model should be is not apparently close. But to my mind, much of this debate seems to miss one important point, how to publish data.
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Tags: Academia, Academic publishing, American Chemical Society, Angewandte Chemie, article processing charge, article processing charges, artificial intelligence, Cognition, Company: RSC, Electronic publishing, G factor, Hybrid open access journal, Knowledge, Michael Dewar, Nature, online era, Open access, Predatory publishing, Publishing, researcher, Royal Society of Chemistry, Scholarly communication, Science, Technology/Internet
Posted in Chemical IT | 2 Comments »
October 18th, 2018
The Royal Society of Chemistry historical group (of which I am a member) organises two or three one day meetings a year. Yesterday the October meeting covered (amongst other themes) the fascinating history of madder and its approximately synthetic equivalent alizarin. Here I add a little to the talk given by Alan Dronsfield on the synthesis of alizarin and the impact this had on the entire industry.
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Tags: Alan Dronsfield, Alizarin, Anthraquinone dyes, Art materials, BASF, Carl Graebe, Carl Gräbe, Carl Liebermann, Carl Theodore Liebermann, Catechols, Colors, cryoEM MicroEM, Dihydroxyanthraquinones, Dye, Mauve, Mauveine, Rapid structure determination of microcrystalline molecular compounds, Royal Society of Chemistry, Shades of violet, William Bragg, William Perkin
Posted in Historical | 1 Comment »