The potential energy surface for a molecule tells us about how it might react. These surfaces have been charted for thousands of reactions using quantum mechanics, and their basic features are thought to be well understood. Coming across an entirely new feature is rare. So what do you make of the following?
Archive for the ‘reaction mechanism’ Category
Intersecting paths in molecular energy surfaces.
Sunday, February 16th, 2014Three-for-one: a pericyclic brain teaser.
Sunday, January 12th, 2014A game one can play with pericyclic reactions is to ask students to identify what type a given example is. So take for example the reaction below.
A simple pericyclic reaction encapsulating the four thermal selection rules.
Thursday, January 2nd, 2014As my previous post hints, I am performing my annual spring-clean of lecture notes on pericyclic reactions. Such reactions, and their stereochemistry, are described by a set of selection rules. I am always on the lookout for a simple example which can most concisely summarise these rules. The (hypothetical) one shown below I think nicely achieves this, and raises some interesting issues in the process.
A curly-arrow pushing manual
Wednesday, December 4th, 2013I 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.
Avoided (pericyclic) anti-aromaticity: Reactions of t-butyl-hydroxycarbene.
Wednesday, November 13th, 2013Not long ago, I described a cyclic carbene in which elevating the carbene lone pair into a π-system transformed it from a formally 4n-antiaromatic π-cycle into a 4n+2 aromatic π-cycle. From an entirely different area of chemistry, another example of this behaviour emerges; Schreiner’s[1] trapping and reactions of t-butyl-hydroxycarbene, as described on Steve Bachrach’s blog. A point I often make is that chemistry is all about connections, and so here I will discuss such a connection.
References
- D. Ley, D. Gerbig, and P.R. Schreiner, "Tunneling control of chemical reactions: C–H insertion versus H-tunneling in tert-butylhydroxycarbene", Chem. Sci., vol. 4, pp. 677-684, 2013. https://doi.org/10.1039/c2sc21555a
Kinetic vs thermodynamic enolization.
Tuesday, November 5th, 2013The concept of kinetic vs thermodynamic control of a reaction is often taught in the context of the enolisation of e.g. 1-methylcyclohexanone as induced by a base. The story goes that at low temperatures (-78°C), the rate of the sterically more hindered thermodynamic enolisation does not compete with the faster kinetic product but that at higher temperatures when an equilibrium is possible, the thermodynamically more stable tetrasubstituted enol is formed. I set out to see if this result can be modelled.
An example of an extreme gauche effect: FSSF.
Saturday, September 21st, 2013The best known example of the gauche effect is 1,2-difluoroethane, which exhibits a relatively small preference of ~0.5 kcal/mol for this conformer over the anti orientation, which is also a minimum. But FSSF, which I discussed in the previous post, beats this hands down! It also, by the way, must surely be the smallest molecule (only four atoms) which could be theoretically resolved into two enantiomers (possibly at say 273K?).‡
The dimer of SF2: small is beautiful (and weird).
Thursday, September 12th, 2013Andy Extance at the Chemistry World blog has picked up on a fascinating article[1] on the dimer of SF2. This molecule has three F atoms on one S, and only one on the other; FSSF3. But all four S-F bonds are of different length. Lindquist and Dunning claim that the minimum energy pathway to dissociation to two SF2 molecules does not involve breaking either the longest or the weakest SF bond. This was too much for me to resist investigating further!
References
- B.A. Lindquist, and T.H. Dunning, "Bonding in FSSF<sub>3</sub>: Breakdown in Bond Length-Strength Correlations and Implications for SF<sub>2</sub> Dimerization", The Journal of Physical Chemistry Letters, vol. 4, pp. 3139-3143, 2013. https://doi.org/10.1021/jz401578h
Coarctate reactions as a third fundamental organic-mechanistic type.
Wednesday, September 4th, 2013According to Herges[1],[2] the mechanism of single-step (concerted) reactions can be divided into three basic types; linear (e.g. substitution, elimination etc), pericyclic (e.g. Diels Alder) and a third much rarer, and hence very often overlooked type that was named coarctate. This is based on the topology of bond redistribution patterns, an explicit real example[3] illustrating:
References
- R. Herges, "Coarctate transition states: the discovery of a reaction principle", Journal of Chemical Information and Computer Sciences, vol. 34, pp. 91-102, 1994. https://doi.org/10.1021/ci00017a011
- B.S. Young, R. Herges, and M.M. Haley, "Coarctate cyclization reactions: a primer", Chemical Communications, vol. 48, pp. 9441, 2012. https://doi.org/10.1039/c2cc34026g
- C. Berger, C. Bresler, U. Dilger, D. Geuenich, R. Herges, H. Röttele, and G. Schröder, "A Spontaneous Fragmentation: From the Criegee Zwitterion to Coarctate Möbius Aromaticity", Angewandte Chemie International Edition, vol. 37, pp. 1850-1853, 1998. https://doi.org/10.1002/(sici)1521-3773(19980803)37:13/14<1850::aid-anie1850>3.0.co;2-b
Experimental evidence for “hidden intermediates”? Epoxidation of ethene by peracid.
Sunday, August 25th, 2013The 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.
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. https://doi.org/10.1021/ar900013p
- H.S. Rzepa, and C. Wentrup, "Mechanistic Diversity in Thermal Fragmentation Reactions: A Computational Exploration of CO and CO<sub>2</sub> Extrusions from Five-Membered Rings", The Journal of Organic Chemistry, vol. 78, pp. 7565-7574, 2013. https://doi.org/10.1021/jo401146k
- 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 <i>m</i>-Chloroperoxybenzoic Acid", The Journal of Organic Chemistry, vol. 64, pp. 196-201, 1998. https://doi.org/10.1021/jo981652x