Archive for the ‘Interesting chemistry’ Category
Monday, 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
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Saturday, February 16th, 2019
The title of this post comes from the site www.crossref.org/members/prep/ Here you can explore how your favourite publisher of scientific articles exposes metadata for their journal.
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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 »
Tuesday, January 22nd, 2019
The Book of Kells is a spectacularly illuminated gospel manuscript dating from around 800AD and held in Trinity College library in Dublin. Some idea of the colours achieved can be seen below.
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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
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Sunday, January 13th, 2019
Linear free energy relationships (LFER) are associated with the dawn of physical organic chemistry in the late 1930s and its objectives in understanding chemical reactivity as measured by reaction rates and equilibria.
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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 »
Thursday, 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
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Friday, 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 »
Sunday, September 30th, 2018
Here is the concluding part of my exploration of a recently published laboratory experiment for undergraduate students.[1] I had previously outlined a possible mechanistic route, identifying TS3 (below) as the first transition state in which C-C bond formation creates two chiral centres. This is followed by a lower energy TS4 where the final stereocentre is formed, accompanied by inversion of configuration of one of the previously formed centres (red below). Now I explore what transition state calculations have to say about the absolute configurations of the final stereocentres in the carbaldehyde product.
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References
- M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (<i>E</i>)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, vol. 95, pp. 1832-1839, 2018. https://doi.org/10.1021/acs.jchemed.7b00566
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Thursday, September 20th, 2018
Recently, the 100th anniversary of the birth of the famous chemist Derek Barton was celebrated with a symposium. One of the many wonderful talks presented was by Tobias Ritter and entitled “Late-stage fluorination for PET imaging” and this resonated for me. The challenge is how to produce C-F bonds under mild conditions quickly so that 18F-labelled substrates can be injected for the PET imaging. Ritter has several recent articles on this theme which you should read.[1],[2].
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References
- P. Tang, W. Wang, and T. Ritter, "Deoxyfluorination of Phenols", Journal of the American Chemical Society, vol. 133, pp. 11482-11484, 2011. https://doi.org/10.1021/ja2048072
- C.N. Neumann, and T. Ritter, "Facile C–F Bond Formation through a Concerted Nucleophilic Aromatic Substitution Mediated by the PhenoFluor Reagent", Accounts of Chemical Research, vol. 50, pp. 2822-2833, 2017. https://doi.org/10.1021/acs.accounts.7b00413
Tags:Antimatter, Barton, Chemistry, Derek Barton, Fluorine, Medical physics, Medicinal radiochemistry, Natural sciences, Neuroimaging, Physical sciences, Positron emission tomography, Radiation therapy, Ritter, Tobias Ritter
Posted in Interesting chemistry | 9 Comments »
Saturday, September 1st, 2018
I am exploring the fascinating diverse facets of a recently published laboratory experiment for undergraduate students.[1] Previously I looked at a possible mechanistic route for the reaction between an enal (a conjugated aldehyde-alkene) and benzyl chloride catalysed by base and a chiral amine, followed by the use of NMR coupling constants to assign relative stereochemistries. Here I take a look at some chiroptical techniques which can be used to assign absolute stereochemistries (configurations).
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References
- M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (<i>E</i>)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, vol. 95, pp. 1832-1839, 2018. https://doi.org/10.1021/acs.jchemed.7b00566
Tags:Absolute configuration, Biochemistry, bulk solutions, chemical transformations, Chemistry, Conformational isomerism, difficult energy difference, gas phase, higher energy forms, Isomer, Isomerism, Nature, Physical organic chemistry, Polarization, spectroscopy, stereochemical product, Stereochemistry, Stereoisomerism, Vibrational circular dichroism
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Sunday, August 26th, 2018
In the previous post, I investigated the mechanism of cyclopropanation of an enal using a benzylic chloride using a quantum chemistry based procedure. Here I take a look at the NMR spectra of the resulting cyclopropane products, with an evaluation of the original stereochemical assignments.[1]
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References
- M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (<i>E</i>)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, vol. 95, pp. 1832-1839, 2018. https://doi.org/10.1021/acs.jchemed.7b00566
Tags:Benzyl group, Chemistry, Cyclopropanation, cyclopropane products, Cyclopropanes, Nuclear magnetic resonance, Organic chemistry, Organic reactions, Protecting groups
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