Posts Tagged ‘Stereochemistry’

How does methane invert (its configuration)?

Thursday, March 16th, 2017
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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?

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A periodic table for anomeric centres.

Saturday, August 6th, 2016
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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.

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Anomeric effects at boron, silicon and phosphorus.

Friday, July 1st, 2016
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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

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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
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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?

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

Wednesday, May 25th, 2016
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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.

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VSEPR Theory: A closer look at trifluorothionitrile, NSF3.

Saturday, January 16th, 2016
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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.

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A visualization of the anomeric effect from crystal structures.

Thursday, August 27th, 2015
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The anomeric effect is best known in sugars, occuring in sub-structures such as RO-C-OR. Its origins relate to how the lone pairs on each oxygen atom align with the adjacent C-O bonds. When the alignment is 180°, one oxygen lone pair can donate into the C-O σ* empty orbital and a stabilisation occurs. Here I explore whether crystal structures reflect this effect.

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