Archive for the ‘Curly arrows’ 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
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W.H. Graham, "The Halogenation of Amidines. I. Synthesis of 3-Halo- and Other Negatively Substituted Diazirines1", Journal of the American Chemical Society, vol. 87, pp. 4396-4397, 1965. http://dx.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 »
Wednesday, December 4th, 2013
I have several times used arrow pushing on these blogs. But since the rules for this convention appear to be largely informal, and there appears to be no definitive statement of them, I thought I would try to produce this for our students. This effort is here shared on my blog. It is what I refer to as the standard version; an advanced version is in preparation. Such formality might come as a surprise to some; arrow-pushing is often regarded as far too approximate to succumb to any definition, although it is of course often examined.
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Posted in Curly arrows, General, reaction mechanism | 6 Comments »
Sunday, August 25th, 2013
The concept of a “hidden intermediate” in a reaction pathway has been promoted by Dieter Cremer[1] and much invoked on this blog. When I used this term in a recent article of ours[2], a referee tried to object, saying it was not in common use in chemistry. The term clearly has an image problem. A colleague recently sent me an article to read (thanks Chris!) about isotope effects in the epoxidation of ethene[3] and there I discovered a nice example of hidden intermediates which I share with you now.
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References
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E. Kraka, and D. Cremer, "Computational Analysis of the Mechanism of Chemical Reactions in Terms of Reaction Phases: Hidden Intermediates and Hidden Transition States", Accounts of Chemical Research, vol. 43, pp. 591-601, 2010. http://dx.doi.org/10.1021/ar900013p
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H.S. Rzepa, and C. Wentrup, "Mechanistic Diversity in Thermal Fragmentation Reactions: A Computational Exploration of CO and CO2 Extrusions from Five-Membered Rings", The Journal of Organic Chemistry, vol. 78, pp. 7565-7574, 2013. http://dx.doi.org/10.1021/jo401146k
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T. Koerner, H. Slebocka-Tilk, and R.S. Brown, "Experimental Investigation of the Primary and Secondary Deuterium Kinetic Isotope Effects for Epoxidation of Alkenes and Ethylene withm-Chloroperoxybenzoic Acid", The Journal of Organic Chemistry, vol. 64, pp. 196-201, 1999. http://dx.doi.org/10.1021/jo981652x
Tags:activation free energy, arrow pushing, curly arrow, dichloromethane solution, Dieter Cremer, hidden intermediate, model, using per-ethanoic acid
Posted in Curly arrows, reaction mechanism | 2 Comments »
Wednesday, June 12th, 2013
A little while ago, I set out some interpretations of how to push curly arrows. I also appreciate that some theoretically oriented colleagues regard the technique as neither useful nor in the least rigorous, whereas towards the other extreme many synthetically minded chemists view the ability to push a reasonable set of arrows for a proposed mechanism as of itself constituting evidence in its favour.[1] Like any language for expressing ideas, the tool needs a grammar (rules) and a vocabulary, and perhaps also an ability to carry ambiguity. These thoughts surfaced again via a question asked of me by a student: “is the mechanism for the hydrogens in protonated benzene whizzing around the ring a [1,2] or a [1,6] pericyclic sigmatropic shift?”.
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References
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M.J. Gomes, L.F. Pinto, P.M. Glória, H.S. Rzepa, S. Prabhakar, and A.M. Lobo, "N-heteroatom substitution effect in 3-aza-cope rearrangements", Chemistry Central Journal, vol. 7, pp. 94, 2013. http://dx.doi.org/10.1186/1752-153X-7-94
Tags:first arrow-head, Reaction Mechanism, Tutorial material
Posted in Curly arrows | 8 Comments »
Monday, July 23rd, 2012
Recollect, Robinson was trying to explain why the nitroso group appears to be an o/p director of aromatic electrophilic substitution. Using σ/π orthogonality, I suggested that the (first ever) curly arrows as he drew them could not be the complete story, and that a transition state analysis would be needed. Here it is.
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Tags:free energy activation barrier, Historical, σ/π orthogonality, nitrosyl, non-polar media, o/p director, o/p director of aromatic electrophilic substitution, Reaction Mechanism, Tutorial material
Posted in Curly arrows, Interesting chemistry | 8 Comments »
Friday, July 20th, 2012
Little did I imagine, when I discovered the original example of using curly arrows to express mechanism, that the molecule described there might be rather too anarchic to use in my introductory tutorials on organic chemistry. Why? It simply breaks the (it has to be said to some extent informal) rules! Consider the dimerisation of nitrosomethane (in fact a well-known equilibrium).
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Tags:dimer, Reaction Mechanism, Tutorial material
Posted in Curly arrows | 3 Comments »
Friday, July 20th, 2012
I was first taught curly arrow pushing in 1968, and have myself taught it to many a generation of student since. But the other day, I learnt something new. Nick Greeves was kind enough to send me this link to the origin of curly arrow pushing in organic chemistry, where the following diagram is shown and Alan Dronsfield sent me two articles he co-wrote on the topic (T. M. Brown, A. T. Dronsfield and P. J. T Morris, Education in Chemistry, 2001, 38, 102-104, 107 and 2003, 40, 129-134); thanks to both of them.
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Tags:Alan Dronsfield, Historical, Indiana, Nick Greeves, Reaction Mechanism, Robert Robinson, Tutorial material
Posted in Curly arrows | 12 Comments »