Comments for Henry Rzepa

Comment on Woodward’s symmetry considerations applied to electrocyclic reactions. by Ryan

Ryan — Wed, 22 May 2013 12:37:04 +0000

Wiki is one of my usual sources, it indeed gives wrong structure about TosMIC this time. Below are other sources for Van-Leusen and Ugi reactions.
http://www.organic-chemistry.org/namedreactions/van-leusen-reaction.sham
http://www.organic-chemistry.org/namedreactions/ugi-reaction.shtm
I also use “Strategic Applications of Named Reactions in Organic Synthesis” as my mechanism check book. Three sources have three different descriptions of isocyanides: -C=N-R, :C=NCH2Tos -C@N+-R(@ triple bond).Also the different mechanism for Ugi.

Comment on Woodward’s symmetry considerations applied to electrocyclic reactions. by Henry Rzepa

Henry Rzepa — Wed, 22 May 2013 10:01:15 +0000

I looked up the Van Leusen reaction in the usual source (is it the one you looked up?), finding a serious error there in the mechanistic diagram. TosMIC is tosyl methyl isocyanide, TsCH2NC, but the Wiki entry on this reaction shows it as TSCH2CN. This does not help in understanding what is going on.

Comment on Solid carbon dioxide: hexacoordinate carbon? by Henry Rzepa

Henry Rzepa — Wed, 22 May 2013 06:38:24 +0000

I note here two recent publications (doi: 10.1073/pnas.1118791109 and 10.1103/PhysRevLett.108.125701) where the structure of carbon dioxide at very high pressures has been solved (CO2-V). It contains tetrahedral CO4 units with no remaining C=O double bonds.

Comment on Woodward’s symmetry considerations applied to electrocyclic reactions. by Ryan

Ryan — Tue, 21 May 2013 15:36:51 +0000

Hi Professor,

Some questions not involving Woodward.

Have you ever run some calculations about isocyanide compound?

I’m confused with isocyanide’s role in two Named Reactions, Van Leusen and Ugi FCR.

In Van Leusen, it acts as an electrophile: however, in Ugi, it acts as a nucloephile.

Is isocyanide a carbene-like compound? BTW, the mechanism of Van Leusen is quite complex and obscure.

Please take a look if you have time.

Comment on The mechanism of ester hydrolysis via alkyl oxygen cleavage under a quantum microscope by Ryan

Ryan — Tue, 21 May 2013 14:34:18 +0000

Recently, we used LiI/MeCN to cleave the methyl ester, this reaction should pass through the methyl oxygen cleavage, I- is a much better nucleophile than H2O.

Comment on Atropisomerism in Taxol. An apparently simple bond rotation? by Woodward’s symmetry considerations applied to electrocyclic reactions. « Henry Rzepa

Mon, 20 May 2013 18:58:30 +0000

[...] of this transition state, I illustrate another isomerism that 6 can undertake; a low-barrier atropisomerism to form 9, followed by another reaction with a relatively low barrier, 9 ↠ 7 to give the [...]

Comment on Hafnium and Niels Bohr by Woodward’s symmetry considerations applied to electrocyclic reactions. « Henry Rzepa

Mon, 20 May 2013 18:56:16 +0000

[...] theories in chemistry write a personal and anecdotal account of their work. Niels Bohr[1] was one such and four decades later Robert Woodward wrote “The conservation of orbital symmetry” [...]

Comment on A sideways look at the mechanism of ester hydrolysis. by Qadir Timerghazin

Qadir Timerghazin — Thu, 16 May 2013 23:43:41 +0000

Apropos: http://pubs.acs.org/doi/abs/10.1021/jp311504d “Revisiting the Mechanism of Neutral Hydrolysis of Esters: Water Autoionization Mechanisms with Acid or Base Initiation Pathways”

Comment on The importance of being complete. by Au and Pt π-complexes of cyclobutadiene. « Henry Rzepa

Au and Pt π-complexes of cyclobutadiene. « Henry Rzepa — Thu, 16 May 2013 08:42:47 +0000

[...] this time is eliminated by forming an allyl cation on the ring. I have described this mode in another post, commenting on the effect when a guanidinium cation interacts with [...]

Comment on The π-complex theory of metal-alkene compounds. by Au and Pt π-complexes of cyclobutadiene. « Henry Rzepa

Au and Pt π-complexes of cyclobutadiene. « Henry Rzepa — Wed, 15 May 2013 19:01:46 +0000

[...] Chemistry with a twist « The π-complex theory of metal-alkene compounds. [...]

Comment on Concerted 1,4-addition of thioacetic acid: a (requested) reality check. by Henry Rzepa

Henry Rzepa — Tue, 14 May 2013 07:55:50 +0000

I have computed kinetic isotope effects for 2H replacing S-H and for 13C on the carbon where a S-C bond forms for the crotonaldehyde reaction (R=Me). I would first note that

1. The S-H-O angle is 162°, it is almost linear, despite being part of a 6-membered ring.
2. At the transition state, the proton has essentially completed transfer (rSH 2.007Å, rOH 1.023Å), and it is the C-S bond that is actually forming.

The KIE come out as follows:
1H/2H = 1.76 (small)
12C/13C 1.024 (medium).

If this can be verified by experiment, it would strengthen the case for the concerted 1,4 addition across the S-H bond.

Comment on Ferrocene by The π-complex theory of metal-alkene compounds. « Henry Rzepa

The π-complex theory of metal-alkene compounds. « Henry Rzepa — Mon, 13 May 2013 19:08:25 +0000

[...] period 1951–1954 was a golden one for structural chemistry; proteins, DNA, Ferrocene (1952) and the one I discuss here, a bonding model for Zeise’s salt [...]

Comment on Concerted 1,4-addition of thioacetic acid: a (requested) reality check. by Henry Rzepa

Henry Rzepa — Mon, 13 May 2013 18:28:28 +0000

Perhaps kinetic isotope effects (2H, 13C ?) might further probe whether the reaction for either system is concerted or open-chain?

Comment on Concerted 1,4-addition of thioacetic acid: a (requested) reality check. by Look@s

Look@s — Mon, 13 May 2013 17:00:47 +0000

Henry, thanks a lot, this is very nice. The statement “…this scheme … recommends itself for evaluation by in silico methods“ had been partly inspired by your blog. It is good to know that the concerted mechanism is "making sense" here. In view of the stereochemical result (for crotonaldehyde), this makes me believe that the concerted mechanism is truly operating. In case of acrolein, there must be another open-chain mechanism operating in parallel, which leads to some (E)-product in acetone (E/Z ≈ 1:4) or considerably more in polar donor-solvents (MeOH, E/Z = 2:1; DMSO, 6:1). The lower barrier for the concerted mechanism with crotonaldehyde is an interesting result, which I would not have expected, by intuition.

Comment on Hidden intermediates in the (acid catalysed) ring opening of propene epoxide. by Transition states for the (base) catalysed ring opening of propene epoxide. « Henry Rzepa

Wed, 08 May 2013 18:30:34 +0000

[...] Chemistry with a twist « Hidden intermediates in the (acid catalysed) ring opening of propene epoxide. [...]

Comment on Why diphenyl peroxide does not exist. by Henry Rzepa

Henry Rzepa — Tue, 07 May 2013 05:21:29 +0000

The above question prompts me to remind everyone of “CCL” (as it is known to its friends, or computational chemistry list“). It is a remarkable 22 years old now and thousands of questions such as the above have both been posted and often answered there. I suspect many of the current generation of computational chemists have learnt (at least in part) their trade there.

There is quite a lot there about IRCs, although much of it is how about to run one!

Comment on Why diphenyl peroxide does not exist. by Ryan

Ryan — Mon, 06 May 2013 09:00:11 +0000

Thanks very much for the clarification. Could you tell me where to get a short introduction about IRC? I didn’t find enough information on Wikipedia.
I have two organic books about mechanism, they often give different mechanism on the same reaction which makes me confused. Theory study is very helpful to clarify the real mechanism.

Comment on Why diphenyl peroxide does not exist. by Henry Rzepa

Henry Rzepa — Sun, 05 May 2013 07:05:21 +0000

It is the integrated progress along the reaction coordinate, centred at the transition state, which is zero, and leading to either the reactant in one direction, or to the product in the other. The sign of the IRC is in effect random; the value has no great meaning.

Comment on Why diphenyl peroxide does not exist. by Ryan

Ryan — Sat, 04 May 2013 16:11:03 +0000

Hi, professor Rzepa, what’s the meanig of horizontal coordinate in IRC?
Molecular Distance? Why can it be minus?

Comment on X-ray analysis and absolute configuration determination using porous complexes. by Ryan

Ryan — Tue, 30 Apr 2013 11:09:51 +0000

Their work is a huge contribution to the science of structure and configuration determination! Smart method.