Posts Tagged ‘activation free energy’
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 »
Saturday, July 11th, 2015
Previously on the kinetic isotope effects for the Baeyer-Villiger reaction, I was discussing whether a realistic computed model could be constructed for the mechanism. The measured KIE or kinetic isotope effects (along with the approximate rate of the reaction) were to be our reality check. I had used ΔΔG energy differences and then HRR (harmonic rate ratios) to compute[1] the KIE, and Dan Singleton asked if I had included heavy atom tunnelling corrections in the calculation, which I had not. His group has shown these are not negligible for low-barrier reactions such as ring opening of cyclopropyl carbinyl radical.[2] As a prelude to configuring his suggested programs for computing tunnelling (GAUSSRATE and POLYRATE), it was important I learnt how to reproduce his KIE values.[2] Hence the title of this post. Now, read on.
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References
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Rzepa, Henry S.., "KINISOT. A basic program to calculate kinetic isotope effects using normal coordinate analysis of transition state and reactants.", 2015. http://dx.doi.org/10.5281/zenodo.19272
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O.M. Gonzalez-James, X. Zhang, A. Datta, D.A. Hrovat, W.T. Borden, and D.A. Singleton, "Experimental Evidence for Heavy-Atom Tunneling in the Ring-Opening of Cyclopropylcarbinyl Radical from Intramolecular 12C/13C Kinetic Isotope Effects", Journal of the American Chemical Society, vol. 132, pp. 12548-12549, 2010. http://dx.doi.org/10.1021/ja1055593
Tags:activation free energy, Basis set, Dan Singleton, energy differences, gas phase calculation, Kinetic isotope effect, PDF, Physical organic chemistry
Posted in reaction mechanism | 2 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 with m-Chloroperoxybenzoic Acid", The Journal of Organic Chemistry, vol. 64, pp. 196-201, 1998. 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 | 3 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.
(more…)
References
-
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 with m-Chloroperoxybenzoic Acid", The Journal of Organic Chemistry, vol. 64, pp. 196-201, 1998. 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 »
Saturday, December 11th, 2010
Janus was the mythological Roman god depicted as having two heads facing opposite directions, looking simultaneously into the past and the future. Some of the most ancient (i.e. 19th century) known reactions can be considered part of a chemical mythology; perhaps it is time for a Janus-like look into their future.
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Tags:activation free energy, benzonitrile product, chemical mythology, coloured solutions, cyano, diazo, diazonium, free energy, Henry Rzepa, Historical, Ion-Pair Mechanisms, L. A., nitrogen gas
Posted in Interesting chemistry | 3 Comments »