Posts Tagged ‘Functional groups’

Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining.

Saturday, June 18th, 2016

In this post, I pondered upon the C=O infra-red spectroscopic properties of esters, and showed three possible electronic influences:

(more…)

What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group?

Wednesday, May 11th, 2016

I have previously commented on the Bürgi–Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R2N-NR2) are supposed to have enhanced reactivity[1] due to what might be described as buttressing of adjacent lone pairs. Here I focus in on how this might manifest by performing searches of the Cambridge structural database for intermolecular (non-bonded) interactions between X-Y nucleophiles (X,Y= N,O,S) and carbonyl compounds OC(NM)2.

(more…)

References

  1. G. Klopman, K. Tsuda, J. Louis, and R. Davis, "Supernucleophiles—I", Tetrahedron, vol. 26, pp. 4549-4554, 1970. http://dx.doi.org/10.1016/S0040-4020(01)93101-1

Azane oxide, a tautomer of hydroxylamine.

Friday, April 15th, 2016

In the previous post I described how hydronium hydroxide or H3O+…HO, an intermolecular tautomer of water, has recently been observed captured inside an organic cage[1] and how the free-standing species in water can be captured computationally with the help of solvating water bridges. Here I explore azane oxide or H3N+-O, a tautomer of the better known hydroxylamine (H2N-OH).

(more…)

References

  1. M. Stapf, W. Seichter, and M. Mazik, "Unique Hydrogen-Bonded Complex of Hydronium and Hydroxide Ions", Chemistry - A European Journal, vol. 21, pp. 6350-6354, 2015. http://dx.doi.org/10.1002/chem.201406383

Ways to encourage water to protonate an amine: superbasing.

Friday, April 8th, 2016

Previously, I looked at models of how ammonia could be protonated by water to form ammonium hydroxide. The energetic outcome of my model matched the known equilbrium in water as favouring the unprotonated form (pKb ~4.75). I add here two amines for which R=Me3Si and R=CN. The idea is that the first will assist nitrogen protonation by stabilising the positive centre and the second will act in the opposite sense; an exploration if you like of how one might go about computationally designing a non-steric superbasic amine that becomes predominantly protonated when exposed to water (pKb <1) and is thus more basic than hydroxide anion in this medium.

(more…)

I’ve started so I’ll finish. Kinetic isotope effect models for a general acid as a catalyst in the protiodecarboxylation of indoles.

Sunday, January 10th, 2016

Earlier I explored models for the heteroaromatic electrophilic protiodecarboxylation of an 3-substituted indole, focusing on the role of water as the proton transfer and delivery agent. Next, came models for both water and the general base catalysed ionization of indolinones. Here I explore general acid catalysis by evaluating the properties of two possible models for decarboxylation of 3-indole carboxylic acid, one involving proton transfer (PT) from neutral water in the presence of covalent un-ionized HCl (1) and one with PT from a protonated water resulting from ionised HCl (2).

(more…)

π-Resonance in thioamides: a crystallographic “diff” with amides.

Saturday, September 5th, 2015

The previous post explored the structural features of amides. Here I compare the analysis with that for the closely related thioamides.

(more…)

R-X≡X-R: G. N. Lewis’ 100 year old idea.

Friday, May 22nd, 2015

As I have noted elsewhere, Gilbert N. Lewis wrote a famous paper entitled “the atom and the molecule“, the centenary of which is coming up.[1] In a short and rarely commented upon remark, he speculates about the shared electron pair structure of acetylene,  R-X≡X-R (R=H, X=C). It could, he suggests, take up three forms. H-C:::C-H and two more which I show as he drew them. The first of these would now be called a bis-carbene and the second a biradical.

(more…)

References

  1. G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. http://dx.doi.org/10.1021/ja02261a002

The Bürgi–Dunitz angle revisited: a mystery?

Tuesday, May 12th, 2015

The Bürgi–Dunitz angle is one of those memes that most students of organic chemistry remember. It hypothesizes the geometry of attack of a nucleophile on a trigonal unsaturated (sp2) carbon in a molecule such as ketone, aldehyde, ester, and amide carbonyl. Its value obviously depends on the exact system, but is generally taken to be in the range 105-107°. A very good test of this approach is to search the crystal structure database (this was how it was originally established[1]).

(more…)

References

  1. H. B:urgi, J. Dunitz, J. Lehn, and G. Wipff, "Stereochemistry of reaction paths at carbonyl centres", Tetrahedron, vol. 30, pp. 1563-1572, 1974. http://dx.doi.org/10.1016/S0040-4020(01)90678-7

A new way of exploring the directing influence of (electron donating) substituents on benzene.

Friday, April 17th, 2015

The knowledge that substituents on a benzene ring direct an electrophile engaged in a ring substitution reaction according to whether they withdraw or donate electrons is very old.[1] Introductory organic chemistry tells us that electron donating substituents promote the ortho and para positions over the meta. Here I try to recover some of this information by searching crystal structures.

(more…)

References

  1. H.E. Armstrong, "XXVIII.—An explanation of the laws which govern substitution in the case of benzenoid compounds", J. Chem. Soc., Trans., vol. 51, pp. 258-268, 1887. http://dx.doi.org/10.1039/CT8875100258