Posts Tagged ‘Reaction Mechanism’

Mechanistic arrow pushing. A proposed addition to its rules.

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.[cite]10.1186/1752-153X-7-94[/cite] 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?”. 


Mechanism of the Van Leusen reaction.

Wednesday, May 29th, 2013

This is a follow-up to comment posted by Ryan, who asked about isocyanide’s role (in the form of the anion of tosyl isocyanide, or TosMIC): “In Van Leusen, it (the isocyanide) acts as an electrophile”. The Wikipedia article (recently updated by myself) shows nucleophilic attack by an oxy-anion on the carbon of the C≡N group, with the isocyanide group acting as the acceptor of these electrons (in other words, the electrophile). In the form shown below, one negatively charged atom appears to be attacking another also carrying a negative charge. Surely this breaks the rules that like charges repel? So we shall investigate to see if this really happens.


Another Woodward pericyclic example dissected: all is not what it seems.

Wednesday, May 22nd, 2013

Here is another example gleaned from that Woodward essay of 1967 (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249), where all might not be what it seems.


Woodward’s symmetry considerations applied to electrocyclic reactions.

Monday, May 20th, 2013

Sometimes the originators of seminal theories in chemistry write a personal and anecdotal account of their work. Niels Bohr[cite]10.1007/BF01326955[/cite] was one such and four decades later Robert Woodward wrote “The conservation of orbital symmetry” (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249; it is not online and so no doi can be given). Much interesting chemistry is described there, but (like Bohr in his article), Woodward lists no citations at the end, merely giving attributions by name. Thus the following chemistry (p 236 of this article) is attributed to a Professor Fonken, and goes as follows (excluding the structure in red):


Concerted 1,4-addition of thioacetic acid: a (requested) reality check.

Saturday, May 11th, 2013

Lukas, who occasionally comments on this blog, sent me the following challenge. In a recent article[cite]10.1021/jo3021709[/cite] he had proposed that the stereochemical outcome (Z) of reaction between a butenal and thioacetic acid as shown below arose by an unusual concerted cycloaddtion involving an S-H bond. He wrote in the article “…this scheme … recommends itself for evaluation by in silico methods“. I asked if the answer could be posted here, and he agreed. So here it is.


Transition states for the (base) catalysed ring opening of propene epoxide.

Wednesday, May 8th, 2013

The previous post described how the acid catalysed ring opening of propene epoxide by an alcohol (methanol) is preceded by pre-protonation of the epoxide oxygen to form a “hidden intermediate” on the concerted intrinsic reaction pathway to ring opening. Here I take a look at the mechanism where a strong base is present, modelled by tetramethyl ammonium methoxide (R4N+.OMe), for the two isomers R=Me; R’=Me, R”=H and R’=H, R”=Me.


Hidden intermediates in the (acid catalysed) ring opening of propene epoxide.

Monday, May 6th, 2013

In a previous post on the topic, I remarked how the regiospecific ethanolysis of propene epoxide[cite]10.1021/ja01208a047[/cite] could be quickly and simply rationalised by inspecting the localized NBO orbital calculated for either the neutral or the protonated epoxide. This is an application of Hammond’s postulate[[cite]10.1021/ja01607a027[/cite] in extrapolating the properties of a reactant to its reaction transition state. This approach implies that for acid-catalysed hydrolysis, the fully protonated epoxide is a good model for the subsequent transition state. But is this true? Can this postulate be tested? Here goes.


Why diphenyl peroxide does not exist.

Monday, April 29th, 2013

A few posts back, I explored the “benzidine rearrangement” of diphenyl hydrazine. This reaction requires diprotonation to proceed readily, but we then discovered that replacing one NH by an O as in N,O-diphenyl hydroxylamine required only monoprotonation to undergo an equivalent facile rearrangement. So replacing both NHs by O to form diphenyl peroxide (Ph-O-O-Ph) completes this homologous series. I had speculated that PhNHOPh might exist if all traces of catalytic acid were removed, but could the same be done to PhOOPh? Not if it continues the trend and requires no prior protonation at all!


How to predict the regioselectivity of epoxide ring opening.

Sunday, April 28th, 2013

I recently got an email from a student asking about the best way of rationalising epoxide ring opening using some form of molecule orbitals. This reminded me of the famous experiment involving propene epoxide.[cite]10.1021/ja01208a047[/cite]


Intermediates in oxime formation from hydroxylamine and propanone: now you see them, now you don’t.

Sunday, April 14th, 2013

A recent theme here has been to subject to scrutiny well-known mechanisms supposedly involving intermediates. These transients can often involve the creation/annihilation of charge separation resulting from  proton transfers, something that a cyclic mechanism can avoid. Here I revisit the formation of an oxime from hydroxylamine and propanone, but with one change. In the earlier post, I used two molecules of water to achieve the desired proton transfer. Now I look to see what effect replacing those two water molecules by a guanidine has.NH2OH+Guanidine