Posts Tagged ‘Lone pair’
Sunday, November 12th, 2017
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…)
Tags:Chemical bond, chemical bonding, Chemistry, Chlorine, Covalent bond, Lone pair, Oxidizing agents, Quantum chemistry, Stereochemistry, Valence, VSEPR theory
Posted in Chemical IT, Hypervalency | 5 Comments »
Monday, August 8th, 2016
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…)
Tags:Anomer, Anomeric effect, Atomic orbital, Carbohydrate chemistry, Carbohydrates, Chemical bond, chemical bonding, Chemistry, Hydrogen bond, interaction energy, Lone pair, Physical organic chemistry, Quantum chemistry
Posted in Interesting chemistry | No Comments »
Saturday, August 6th, 2016
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…)
Tags:Acetals, Alkane stereochemistry, Anomer, Anomeric effect, Atomic orbital, Carbohydrate chemistry, Carbohydrates, Chemical bond, Chemistry, interaction energy, Lone pair, Physical organic chemistry, Stereochemistry
Posted in crystal_structure_mining, Interesting chemistry | No Comments »
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…)
Tags:Acid, Acid dissociation constant, Amide, Amine, Ammonia, Ammonium, Bases, City: Cambridge, energy, from non-protic solution, Functional groups, Hydrogen bond, Hydroxide, Lone pair, metal, Nitrile, relative free energy, search query
Posted in General, Interesting chemistry | 2 Comments »
Saturday, January 16th, 2016
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…)
Tags:Chemical bond, chemical bonding, Electron, Lone pair, Molecular geometry, Octet rule, Quantum chemistry, Stereochemistry, Tetrahedral molecular geometry, Theoretical chemistry, Valence, VSEPR theory
Posted in Hypervalency | 110 Comments »
Thursday, August 27th, 2015
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…)
Tags:Alkane stereochemistry, Anomeric effect, Carbohydrate chemistry, Carbohydrates, Carbon–oxygen bond, Chemical bond, Ether, Lone pair, Physical organic chemistry, Quantum chemistry, Stereochemistry, Technology/Internet
Posted in Chemical IT, crystal_structure_mining | No Comments »