Posts Tagged ‘Stereoelectronic effect’

Stereoelectronic effects galore: bis(trifluoromethyl)trioxide.

Thursday, August 4th, 2016

Here is a little molecule that can be said to be pretty electron rich. There are lots of lone pairs present, and not a few electron-deficient σ-bonds. I thought it might be fun to look at the stereoelectronic interactions set up in this little system.

Trioxide

Known as ZEYDOW in the crystal structure database[1] (this species has a melting point of -138C, and its no trivial matter to measure x-ray diffraction of such a crystal!); a ωB97XD/Def2-TZVPP calculation is used to quantify the electron density [2] and this is then subjected to localisation using the ELF function. The little purple spheres represent so-called monosynaptic electron basins, or lone pairs as we might rather loosely call them (pair is not always an accurate term). 

zeydow

How these “lone pairs” act as electron donors into empty σ* acceptors can be quantified using NBO theory. The following table shows as many as 24 strong interactions (> 10 kcal/mol).  This now augments my previous post on “Anomeric effects at carbon involving lone pairs originating from one or two nitrogens” and represents an example of “Anomeric effects at oxygen involving lone pairs originating from oxygen”.

The final two entries originate from lone pairs on the central oxygen, donating approximately antiperiplanar (~160°) into the O-CF3 antibonds, but with only a low value of the E(2) interaction energy. These two lone pairs are curiously inert.

Lone pair donor σ-acceptor NBO E(2) energy
On F: 16,17,18,19,25,35,36,39,40,41,43,45 C-F 18-20
On F: 26,34,37,39,42,44 C-O 11-18
On O: 27,28,24,33 C-F 13-16
On O: 27,33 C-O 13
On O: 30,31 C-O 3.5

Apart from this curious molecule, there are few other examples of the R-O-O-O-R functional group,[3] but this one did catch my eye,[4] largely because it was retrieved from a search specification of R-O-O-O-R. The central oxygen apparently supports six O-O bonds, as well as three hydrogens. It is nothing of the sort of course. Reading the text reveals it is really three O…H-O bonds, disordered into two equally probable positions. There are no O-O bonds present at all, which reminds us we must always subject structures derived from x-ray crystallography to a chemical reality check.
yocsis

References

  1. K.I. Gobbato, H. Oberhammer, M.F. Klapdor, D. Mootz, W. Poll, S.E. Ulic, and H. Willner, "Bis(trifluoromethyl)trioxide: First Structure of a Straight‐Chain Trioxide", Angewandte Chemie International Edition in English, vol. 34, pp. 2244-2245, 1995. https://doi.org/10.1002/anie.199522441
  2. H.S. Rzepa, "C 2 F 6 O 3", 2016. https://doi.org/10.14469/ch/195291
  3. Pernice, H.., Berkei, M.., Henkel, G.., Willner, H.., Arguello, G.A.., McKee, M.L.., and Webb, T.R.., "CCDC 224327: Experimental Crystal Structure Determination", 2004. https://doi.org/10.5517/cc7jfcj
  4. J.L. Atwood, S.G. Bott, P.C. Junk, and M.T. May, "Liquid clathrate media containing transition metal halocarbonyl anions; formation and crystal structures of [K+ · 18-crown-6][Cr(CO)5Cl], [H3O+ · 18-crown-6][W(CO)5Cl], [H3O+ · 18-crown-6][W(CO)4Cl3], and [H2O · bis-aza-18-crown-6 · (H+)2][W(CO)4Cl3]2", Journal of Organometallic Chemistry, vol. 487, pp. 7-15, 1995. https://doi.org/10.1016/0022-328x(94)05072-j

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Posted in crystal_structure_mining, Interesting chemistry | No Comments »

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

Monday, May 30th, 2016

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?

The search query is shown above results in 394 hits (May 2016) and is presented with the three variables in the query plotted as below, with the O-4A-O angle indicated by colour (red ~ 180°; blue ~90° and green ~120°).

  1. The cluster at distances of 4A-O of ~1.9Å represents silicon compounds, and tends to suggest that the pair of distances 4A-O are quite similar in value. The angles correspond to a di-axial arrangement around the silicon. In this scenario, one might imagine a stereoelectronic effect similar to the anomeric effect when 4A = C operates and which has the potential to strengthen both di-axial oxygens.
  2. The bulk of the points come at higher 4A-O distances of > 2.1Å and consist mostly of 4A = Sn. There are two a clear-cut distributions, one for angles of ~180° and a separate one for angles of ~90° and both are qualitatively different from the Si distribution. The 180° set corresponds to a di-axial arrangement for the oxygens, whereas the 90° set suggests an axial-equatorial geometry. Both distributions have prominent tails which reveal that as one 4A-O distance shortens, the other lengthens, equivalent to asymmetric anomeric effects at  O-C-O.
  3. Noticeably absent are any green points; these would correspond to bond angles of ~120° and hence would correspond to di-equatorial ligands.

This quick exploration (with potential variations that I have not explored above) can be added to the collection of “ten minute explorations” I have described elsewhere.[1]

References

  1. H.S. Rzepa, "Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases", Journal of Chemical Education, vol. 93, pp. 550-554, 2015. https://doi.org/10.1021/acs.jchemed.5b00346

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Posted in Chemical IT, crystal_structure_mining | 3 Comments »