Posts Tagged ‘Functional groups’

Organocatalytic cyclopropanation of an enal: (computational) mechanistic understanding.

Saturday, August 25th, 2018

Symbiosis between computation and experiment is increasingly evident in pedagogic journals such as J. Chemical Education. Thus an example of original laboratory experiments[1],[2] that later became twinned with a computational counterpart.[3] So when I spotted this recent lab experiment[4] I felt another twinning approaching.

(more…)

References

  1. A. Burke, P. Dillon, K. Martin, and T.W. Hanks, "Catalytic Asymmetric Epoxidation Using a Fructose-Derived Catalyst", Journal of Chemical Education, vol. 77, pp. 271, 2000. http://dx.doi.org/10.1021/ed077p271
  2. J. Hanson, "Synthesis and Use of Jacobsen's Catalyst: Enantioselective Epoxidation in the Introductory Organic Laboratory", Journal of Chemical Education, vol. 78, pp. 1266, 2001. http://dx.doi.org/10.1021/ed078p1266
  3. K.K.(. Hii, H.S. Rzepa, and E.H. Smith, "Asymmetric Epoxidation: A Twinned Laboratory and Molecular Modeling Experiment for Upper-Level Organic Chemistry Students", Journal of Chemical Education, vol. 92, pp. 1385-1389, 2015. http://dx.doi.org/10.1021/ed500398e
  4. M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (E)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, vol. 95, pp. 1832-1839, 2018. http://dx.doi.org/10.1021/acs.jchemed.7b00566

The “White City Trio” – The formation of an amide from an acid and an amine in non-polar solution (updated).

Wednesday, August 8th, 2018

White City is a small area in west london created as an exhibition site in 1908, morphing over the years into an Olympic games venue, a greyhound track, the home nearby of the BBC (British Broadcasting Corporation) and most recently the new western campus for Imperial College London. The first Imperial department to move into the MSRH (Molecular Sciences Research Hub) building is chemistry. As a personal celebration of this occasion, I here dedicate three transition states located during my first week of occupancy there, naming them the White City trio following earlier inspiration by a string trio and their own instruments.

(more…)

Are diazomethanes hypervalent molecules? An attempt into more insight by more “tuning” with substituents.

Tuesday, December 26th, 2017

Recollect the suggestion that diazomethane has hypervalent character[1]. When I looked into this, I came to the conclusion that it probably was mildly hypervalent, but on carbon and not nitrogen. Here I try some variations with substituents to see what light if any this casts.

(more…)

References

  1. M.C. Durrant, "A quantitative definition of hypervalency", Chemical Science, vol. 6, pp. 6614-6623, 2015. http://dx.doi.org/10.1039/C5SC02076J

π-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach?

Monday, April 17th, 2017

Following on from my re-investigation of close hydrogen bonding contacts to the π-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469/hpc/2478) is similar to the previous one:

(more…)

The conformation of carboxylic acids revealed.

Tuesday, April 11th, 2017

Following my conformational exploration of enols, here is one about a much more common molecule, a carboxylic acid.

(more…)

σ or π nucleophilic reactivity of imines? A mechanistic reality check using substituents.

Sunday, October 9th, 2016

Previously, a mechanistic twist to the oxidation of imines using peracid had emerged. Time to see how substituents respond to this mechanism.

(more…)

σ or π nucleophilic reactivity of imines? A mechanistic twist emerges.

Wednesday, September 28th, 2016

The story so far. Imines react with a peracid to form either a nitrone (σ-nucleophile) or an oxaziridine (π-nucleophile).[1] The balance between the two is on an experimental knife-edge, being strongly influenced by substituents on the imine. Modelling these reactions using the “normal” mechanism for peracid oxidation did not reproduce this knife-edge, with ΔΔG (π-σ) 16.2 kcal/mol being rather too far from a fine balance.

(more…)

References

  1. D.R. Boyd, P.B. Coulter, N.D. Sharma, W. Jennings, and V.E. Wilson, "Normal, abnormal and pseudo-abnormal reaction pathways for the imine-peroxyacid reaction", Tetrahedron Letters, vol. 26, pp. 1673-1676, 1985. http://dx.doi.org/10.1016/S0040-4039(00)98582-4

More stereoelectronics galore: hexamethylene triperoxide diamine.

Thursday, September 22nd, 2016

Compounds with O-O bonds often have weird properties. For example, artemisinin, which has some fascinating stereoelectronics. Here is another such, recently in the news and known as HMTD (hexamethylene triperoxide diamine). The crystal structure was reported some time ago[1] and the article included an inspection of the computed wavefunction. However this did not look at the potential stereoelectronics in this species, which I now address here.

(more…)

References

  1. A. Wierzbicki, E.A. Salter, E.A. Cioffi, and E.D. Stevens, "Density Functional Theory and X-ray Investigations of P- and M-Hexamethylene Triperoxide Diamine and Its Dialdehyde Derivative", The Journal of Physical Chemistry A, vol. 105, pp. 8763-8768, 2001. http://dx.doi.org/10.1021/jp0123841

What’s in a name? Carbenes: a reality check.

Sunday, September 11th, 2016

To quote from Wikipedia: in chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The most ubiquitous type of carbene of recent times is the one shown below as 1, often referred to as a resonance stabilised or persistent carbene. This type is of interest because of its ability to act as a ligand to an astonishingly wide variety of metals, with many of the resulting complexes being important catalysts. The Wiki page on persistent carbenes shows them throughout in form 1 below, thus reinforcing the belief that they have a valence of two and by implication six (2×2 shared + 2 unshared) electrons in the valence shell of carbon. Here I consider whether this name is really appropriate.

(more…)

How does an OH or NH group approach an aromatic ring to hydrogen bond with its π-face?

Wednesday, June 22nd, 2016

I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and OH or NH groups.

(more…)