Posts Tagged ‘model’
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 »
Monday, September 26th, 2011
To (mis)quote Oscar Wilde again, ““To lose one methyl group may be regarded as a misfortune; to lose both looks like carelessness.” Here, I refer to the (past) tendency of molecular modellers to simplify molecular structures. Thus in 1977, quantum molecular modelling, even at the semi-empirical level, was beset by lost groups. One of my early efforts (DOI: 10.1021/ja00465a005) was selected for study because it had nothing left to lose; the mass spectrometric fragmentation of the radical cations of methane and ethane. Methyl, phenyl and other “large” groups were routinely replaced by hydrogen in order to enable the study. Cations indeed were always of interest to modellers; the relative lack of electrons almost always meant unusual or interesting structures and reactions (including this controversial species, DOI: 10.1021/ja00444a012). Inured to such functional loss, we modellers forgot that (unless in a mass spectrometer), cations have to have a counter anion. Here I explore one example of the model being complete(d).
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Tags:bonded systems, energy difference drops, free energy, Interesting chemistry, model, Oscar, potential energy surface, Steve Bachrach, using perchlorate
Posted in Uncategorised | 7 Comments »
Saturday, February 5th, 2011
In 1953, the model of the DNA molecule led to what has become regarded as the most famous scientific diagram of the 20th century. It had all started 93 years earlier in 1860, at a time when the tetravalency of carbon was only just established (by William Odling) and the concept of atoms as real entities was to remain controversial for another 45 years (for example Faraday, perhaps the most famous scientist alive in 1860 did not believe atoms were real). So the idea of constructing a molecular model from atoms as the basis for understanding chemical behaviour was perhaps bolder than we might think. It is shown below, part of a set built for August Wilhelm von Hofmann as part of the lectures he delivered at the Royal College of Chemistry in London (now Imperial College).
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Tags:and compare the two, chemical behaviour, deficiency, General, Hermann Sachse, Historical, Hofmann, Imperial College, Josef Loschmidt, Loschmidt, model, modern model, molecular model, Odling, Royal College of Chemistry, Royal College of Chemistry in London, Sachse, scientist, Tutorial material, Wilhelm von Hofmann, William Odling
Posted in Uncategorised | 3 Comments »