Posts Tagged ‘Lone pair’

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…)

A periodic table for anomeric centres, this time with quantified interactions.

Monday, August 8th, 2016
No Gravatar

The previous post contained an exploration of the anomeric effect as it occurs at an atom centre X for which the effect is manifest in crystal structures. Here I quantify the effect, by selecting the test molecule MeO-X-OMe, where X is of two types:

(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…)

Ways to encourage water to protonate an amine: superbasing.

Friday, April 8th, 2016
No Gravatar

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…)

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…)

A visualization of the anomeric effect from crystal structures.

Thursday, August 27th, 2015
No Gravatar

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.

(more…)