Posts Tagged ‘chemical phenomena’

A wider look at chlorine trifluoride: crystal structures and data mining.

Friday, June 10th, 2016

A while ago, I explored how the 3-coordinate halogen compound ClF3 is conventionally analyzed using VSEPR (valence shell electron pair repulsion theory). Here I (belatedly) look at other such tri-coordinate halogen compounds using known structures gleaned from the crystal structure database (CSD).

The search query specifies 7A as the central atom, defined with just three bonded (non-metallic) atoms. Initially, if no constraint on any cyclicity in the three 7A-NM bonds is made (and with R < 0.1, no errors, no disorder), the following result emerges.

I have plotted the three angle variables using the X/Y axes above and used colour to indicate the third angle (red = ~180°, blue = ~90°). The clusters show that two of the angles are ~90° and only one is ~180°. There is also a set of blue points (~90°) which show a linear correlation and which can be shown to derive from cyclicity, as the plot below reveals when acyclicity is specified for all three NM-7A bonds.

In this distribution, the two clusters for ANG1 or ANG2 of ~180° are small and compact, but the cluster where both ANG1 and ANG2 are ~90° is much more diffuse. Not all of the points in this cluster show as red (ANG3 ~180°); there are a few cyan or blue examples here too; indicating all three angles are in the range 140-90°. This result is not arising from cyclic constraints. 

This wider look at 3-coordinate compounds in group 17 (the halogens) quickly reveals a class of such molecules where all three angles are relatively small. This suggests that a closer look at the bonding in these systems, especially in terms of VSEPR, might be rewarding!

I end with an equivalent search for group 18 (the noble gases). Although the number of examples is small, all show the two small/one large angle so characteristic of chlorine trifluoride itself. 

The above is I think a good example of (big?) data mining, where one is searching for patterns, and if lucky spotting patterns that deviate from the norm to investigate the possibility of new chemical phenomena.[1] It is also interesting to speculate upon the origins of why two of the clusters shown above are small and compact and the third is much more diffuse.

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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Deviations from planarity of trigonal carbon and from linearity of digonal carbon.

Sunday, September 13th, 2015

Previously, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp3) carbon using crystal structures. Now it is the turn of digonal (sp1) and trigonal (sp2) carbons. 

Firstly, the digonal C≡C case. Attached to each carbon of the C≡C unit are two saturated carbon ligands; this to prevent conjugation from influencing our result. 

Scheme

The result of a search (R-factor < 5%, no errors, no disorder) shows the hotspot at the expected ~180°, but then a fascinating curve as the angle subtended at the digonal carbon angle decreases down to ~110°, with the C≡C bond length gradually increasing. This apparently non-linear behaviour would be interesting to replicate using quantum mechanics.‡

Scheme

Next, the trigonal case. Again, the substituents are 4-coordinate carbons to prevent complicating conjugations.

Scheme

A plot of the C=C distance vs the C-C=C angle brings a surprise. There are four clusters centered at angles of ~132°, 123°, 110° and 94° (cyclobutenes) and a small cluster at ~150°. The C=C distance stays constant at around 1.335Å or shorter, a clear difference with the sp-case. There is perhaps a small outlier collection where the angle is ~108° and the distance ~1.4Å.

Scheme

This plots the dihedral angle subtended at one of the trigonal carbon atoms and measures how non-planar that atom is. There is again no real evidence that the C=C bond length changes as the trigonal centre becomes bent.

Scheme

This dihedral angle measures the twist about the C=C bond; up to about 30° is tolerated, but again there is no clear indication of a systematic change in the C=C length.

Scheme

These analyses reveal general trends on bond lengths induced by distorting the normal coordination around trigonal and digonal carbon atoms. It is only the start of the story of course, since there are plenty of isolated outliers that really should be explored; some may be simply due to undetected crystallographic errors, whilst with others there may lurk interesting or even new chemical phenomena. 

‡Below, the crystal structure result (with the axes transposed) is compared to a closed shell single reference ωB97XD/6-311+G(2df) calculation. Whilst the trend is replicated, it is not quantitative. This is probably because many of the crystal structures are perturbed by other effects, most probably by coordination of a metal and hence back-donation of π-electrons into vacant metal orbitals. The CSD indexing of the structures however retains the C≡C bond notation, even though the bond is no longer truly a triple one. This reinforces the observation I made in the previous post that when searching the CSD, one can stipulate a bond type to constrain the search. But that bond type may be purely nominal and bear little resemblance to the actual electronic structure of the species. There are other issues;  the wave function was constrained to closed shell single determinant. At low angles, the calculation itself is probably not accurate (as can be seen from a kink in the plot, indicating instability).

Scheme

Scheme

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