Posts Tagged ‘Stereochemistry’

VSEPR Theory: Octet-busting or not with trimethyl chlorine, ClMe3.

Sunday, November 12th, 2017
No Gravatar

A few years back, I took a look at the valence-shell electron pair repulsion approach to the geometry of chlorine trifluoride, ClF3 using so-called ELF basins to locate centroids for both the covalent F-Cl bond electrons and the chlorine lone-pair electrons. Whereas the original VSEPR theory talks about five “electron pairs” totalling an octet-busting ten electrons surrounding chlorine, the electron density-based ELF approach located only ~6.8e surrounding the central chlorine and no “octet-busting”. The remaining electrons occupied fluorine lone pairs rather than the shared Cl-F regions. Here I take a look at ClMe3, as induced by the analysis of SeMe6.

(more…)

The di-anion of dilithium (not the Star Trek variety): Another “Hyper-bond”?

Saturday, September 16th, 2017
No Gravatar

Early in 2011, I wrote about how the diatomic molecule Be2 might be persuaded to improve upon its normal unbound state (bond order ~zero) by a double electronic excitation to a strongly bound species. I yesterday updated this post with further suggestions and one of these inspired this follow-up.

(more…)

The conformation of enols: revealed and explained.

Thursday, April 6th, 2017
No Gravatar

Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation.

(more…)

First, hexacoordinate carbon – now pentacoordinate nitrogen?

Saturday, March 25th, 2017
No Gravatar

A few years back I followed a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. That reality was recently confirmed via a crystal structure, DOI:10.5517/CCDC.CSD.CC1M71QM[1]. Here is a similar proposal for penta-coordinate nitrogen.

(more…)

References

  1. M. Malischewski, and K. Seppelt, "Crystal Structure Determination of the Pentagonal-Pyramidal Hexamethylbenzene Dication C6(CH3)62+", Angewandte Chemie International Edition, vol. 56, pp. 368-370, 2016. http://dx.doi.org/10.1002/anie.201608795

How does methane invert (its configuration)?

Thursday, March 16th, 2017
No Gravatar

This is a spin-off from the table I constructed here for further chemical examples of the classical/non-classical norbornyl cation conundrum. One possible entry would include the transition state for inversion of methane via a square planar geometry as compared with e.g. NiH4 for which the square planar motif is its minimum. So is square planar methane a true transition state for inversion (of configuration) of carbon?

(more…)

A periodic table for anomeric centres.

Saturday, August 6th, 2016
No Gravatar

In the last few posts, I have explored the anomeric effect as it occurs at an atom centre X. Here I try to summarise the atoms for which the effect is manifest in crystal structures.

(more…)

Anomeric effects at boron, silicon and phosphorus.

Friday, July 1st, 2016
No Gravatar

The anomeric effect occurs at 4-coordinate (sp3) carbon centres carrying two oxygen substituents and involves an alignment of a lone electron pair on one oxygen with the adjacent C-O σ*-bond of the other oxygen. Here I explore whether other centres can exhibit the phenomenon. I start with 4-coordinate boron, using the crystal structure search definition below (along with R < 0.1, no disorder, no errors).[1]anomeric-bo-sq

(more…)

References

  1. Henry Rzepa., "Anomeric effects at boron, silicon and phosphorus.", 2016. http://dx.doi.org/10.14469/hpc/696

The geometries of 5-coordinate compounds of group 14 elements.

Monday, May 30th, 2016
No Gravatar

This is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C34AO2 with a trigonal bipyramidal geometry. This search arose because of a casual comment I made in the earlier post regarding possible cooperative effects between the two axial ligands (the ones with an angle of ~180 degrees subtended at silicon). Perhaps the geometries might expand upon this comment?

(more…)

The mechanism of silylether deprotection using a tetra-alkyl ammonium fluoride.

Wednesday, May 25th, 2016
No Gravatar

The substitution of a nucleofuge (a good leaving group) by a nucleophile at a carbon centre occurs with inversion of configuration at the carbon, the mechanism being known by the term SN2 (a story I have also told in this post). Such displacement at silicon famously proceeds by a quite different mechanism, which I here quantify with some calculations.

(more…)

VSEPR Theory: A closer look at trifluorothionitrile, NSF3.

Saturday, January 16th, 2016
No Gravatar

The post on applying VSEPR ("valence shell electron pair repulsion") theory to the geometry of ClF3 has proved perennially popular. So here is a follow-up on another little molecue, F3SN. As the name implies, it is often represented with an S≡N bond. Here I take a look at the conventional analysis.

(more…)