Posts Tagged ‘crystal structure search’

Dispersion-induced triplet aromatisation?

Thursday, January 3rd, 2019

There is emerging interest in cyclic conjugated molecules that happen to have triplet spin states and which might be expected to follow a 4n rule for aromaticity.[1] The simplest such system would be the triplet state of cyclobutadiene, for which a non or anti-aromatic singlet state is always found to be lower in energy. Here I explore some crystal structures containing this motif for possible insights.

My search query is shown below, and the search is constrained so that the four substituents are Si, C or H.


The results show three clusters. The top left and bottom right have one long bond length ~1.6Å and the other much shorter at ~1.35Å (Δr ~0.25Å) The central region contains two examples, 2 where the difference between the two lengths is rather smaller and 1 where they are equal.

The first example 1[2] is in fact the di-anion of cyclobutadiene and as a 6π aromatic, one indeed expects the C-C bonds to be equal in length. The second 2 is tetra t-butylcyclobutadiene as reported in 1983.[3] At room temperature the two C-C bond lengths are 1.464 and 1.483Å, at -30°C, 1.466 and 1.492Å and at -150°C 1.441 and 1.526Å (Δr 0.085Å). These results led to the conclusion that this species was not intrinsically square but rectangular, as expected of singlet cyclobutadiene. The equalisation was attributed to equal populations of two disordered rectangular orientations averaging to an approximately square shape at higher temperatures.

But why is the behaviour of this particular cyclobutadiene different from the others in the plot above? Perhaps the answer lies these in the results of the Schreiner group[4], in which the dispersion attractions of substituents such as t-butyl can have substantial and often unexpected effects on the structures of molecules. So it is reasonable to pose the question; could the room temperature bond length differences of 2 be smaller compared with the other more extreme examples as a result of dispersion effects?

Here I have computed the singlet geometry of tetra t-butylcyclobutadiene at the B3LYP+D3BJ/Def2-TZVPP level (i.e. using the D3BJ dispersion correction, FAIR data DOI: 10.14469/hpc/4924). Δr for this singlet state is 0.264Å, larger than apparently from the crystal structure, but in agreement with the other crystal results as seen above.

The origins of the measured structure of 2 must be in the barrier to the automerisation of the singlet state. For normal cyclobutadienes, this must be relatively high since the transition state is presumably anti-aromatic. High enough that the averaging of the two rectangular structures is slow enough that it manifests as two different bond lengths. But in 2, as the temperature of the crystal increases, the bonds become more equal, suggesting a lower barrier to the equalisation than the other examples. This is also supported by the apparent identification of a triplet square state for the tetra-TMS analogue of tetra-tert-butyl cyclobutadiene derivative [5] which again suggests that dispersion might favour a square form over the rectangular one.

To finish, I show the crystal structure search for the 8-ring homologue of cyclobutadiene, plotted for the two adjacent C-C lengths and (in colour) the dihedral angle associated with the three atoms involved and the fourth along the ring. Cluster 1 represents various boat-shaped derivatives with very different C-C bond lengths. Cluster 2 are all ionic, and as per above represent a planar 10π-electron ring. Cluster 3 are mostly “tethered” molecules in which additional rings enforce planarity. 

COT

Unfortunately, none of these derivatives include tert-butyl or TMS derivatives in adjacent positions around the central ring. Perhaps octa(t-Bu)cyclo-octatetraene or its TMS analogue would be interesting molecules to try to synthesize!

References

  1. A. Kostenko, B. Tumanskii, Y. Kobayashi, M. Nakamoto, A. Sekiguchi, and Y. Apeloig, "Spectroscopic Observation of the Triplet Diradical State of a Cyclobutadiene", Angewandte Chemie International Edition, vol. 56, pp. 10183-10187, 2017. https://doi.org/10.1002/anie.201705228
  2. T. Matsuo, T. Mizue, and A. Sekiguchi, "Synthesis and Molecular Structure of a Dilithium Salt of the <i>cis</i>-Diphenylcyclobutadiene Dianion", Chemistry Letters, vol. 29, pp. 896-897, 2000. https://doi.org/10.1246/cl.2000.896
  3. H. Irngartinger, and M. Nixdorf, "Bonding Electron Density Distribution in Tetra‐<i>tert</i>‐butylcyclobutadiene— A Molecule with an Obviously Non‐Square Four‐Membered ring", Angewandte Chemie International Edition in English, vol. 22, pp. 403-404, 1983. https://doi.org/10.1002/anie.198304031
  4. S. Rösel, H. Quanz, C. Logemann, J. Becker, E. Mossou, L. Cañadillas-Delgado, E. Caldeweyher, S. Grimme, and P.R. Schreiner, "London Dispersion Enables the Shortest Intermolecular Hydrocarbon H···H Contact", Journal of the American Chemical Society, vol. 139, pp. 7428-7431, 2017. https://doi.org/10.1021/jacs.7b01879

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Intermolecular atom-atom bonds in crystals? The O…O case.

Saturday, July 25th, 2015

I recently followed this bloggers trail; link1 → link2 to arrive at this delightful short commentary on atom-atom bonds in crystals[1] by Jack Dunitz. Here he discusses that age-old question (to chemists), what is a bond? Even almost 100 years after Gilbert Lewis’ famous analysis,[2] we continue to ponder this question. Indeed, quite a debate on this topic broke out in a recent post here. My eye was caught by one example in Jack’s article: “The close stacking of planar anions, as occurs in salts of croconic acid …far from producing a lowering of the crystal energy, this stacking interaction in itself leads to an increase by several thousand kJ mol−1 arising from Coulombic repulsion between the doubly negatively charged anions” I thought I might explore this point a bit further in this post.

A search query of the Cambridge structure database was defined as below. Two non-bonded oxygen atoms are each attached to one carbon, each oxygen was defined as having one bonded atom (to carbon) and each assigned one negative charge. Addition of the usual constraints of R < 0.05, no errors, no disorder and specifying an intermolecular search produced 103 hits with the distance distribution shown below.

OO-query

O-O

Firstly, you should be aware that the van der Waals radius for oxygen is ~1.5Å, and so any contacts less than 3.0Å become interesting. What becomes particularly exciting is the distinct cluster at ~2.5Å. Could these be ~30 examples of close encounters of the type noted by Dunitz? Well, a control search has to be done, this time for O-H-O motifs, with each OH distance plotted as below:

OHO

The hot-spot occurs when both OH distances are equal at ~1.22Å, or an O…O separation close to 2.45Å. Time to quote Dunitz again “This large destabilization is, of course, more than compensated in the overall energy balance by the large stabilization arising from Coulombic interactions of the croconate anions with the surrounding cations.” In this case of course, the cation is a proton, residing at the half way point between the two oxygens. So two oxygens can indeed approach ~0.5Å closer than the sum of the vdw radii if a proton sits in-between them.

What do we learn? Well, firstly that one should always have a reality check of the results of any crystal structure search. The search did specify that the oxygens be non-bonded but also that they should both carry a negative charge and that both should only have one bonded atom. That should in theory at least have excluded any C-O-H-O-C structures, so why were about 30 such examples found? I can only speculate here, but recollect that 50 years ago when the CSD was founded, hydrogen atoms were rarely identified from the electron density. They were instead placed or “idealised” to where they might be expected. Nowadays any contentious hydrogens are almost always located rather than idealised, but clearly their status as bona-fide atoms is not quite so strong as the rest of the periodic table. So in at least some of these 30 examples with short O…O contacts, we might expect there to lurk a (possibly unrecognised) proton. But one never knows, there may be some real examples of O…O contacts with no such proton intervening. Now these really would be interesting.

Postscript. F is isoelectronic with O(-); below is the same search as defined above, but for non-bonded CF…FC approaches. F---F

The vdw radius of F is 1.45Å hence any non-bonded contact <2.9Å is worth taking a look at. But notice the small cluster of about 10 compounds for which the value is ~2.15Å. The F-H-F plot shows a hot spot at ~2.3 for the F…F separation, but there are zero hits for CF-H-FC. So these ten hits are indeed tantalising.

References

  1. J.D. Dunitz, "Intermolecular atom–atom bonds in crystals?", IUCrJ, vol. 2, pp. 157-158, 2015. https://doi.org/10.1107/s2052252515002006
  2. G.N. Lewis, "THE ATOM AND THE MOLECULE.", Journal of the American Chemical Society, vol. 38, pp. 762-785, 1916. https://doi.org/10.1021/ja02261a002

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Halogen bonds 4: The strongest (?) halogen bond.

Sunday, December 7th, 2014

Continuing my hunt, here is a candidate for a strong(est?) halogen bond, this time between Se and I.[1].
OXSELI
The features of interest include:

  1. The six-membered ring is in the chair conformation.
  2. The (relatively enormous) I…I substituent is axial!
  3. It is attached to the Se rather than the O.
  4. The Se…I distance is 2.75Å, some 1.13Å shorter than the combined atom ver der Waals radii (1.90 + 1.98 = 3.88)
  5. The Wiberg bond index is 0.42 for the Se-I bond and 0.63 for the I-I bond (at the crystal geometry). It is tending towards a symmetrical disposition of the central iodine (a feat also achieved by the iodine in the NI3 complex).
  6. The NBO E(2) perturbation involving donation from the Se lone pair into the I-I antibond is 77 kcal/mol, almost twice the value of the one involving DABCO…I-I and way above the values found for the related hydrogen bond.
  7. The B3LYP+D3/Def2-TZVPP+PP(I) optimised structure expands the Se-I bond distance to 3.04 and contracts the I-I distance to 2.81Å indicating (as with DABCO…I-I) that there may be compression of this bond induced by the lattice.
  8. The NCI surface shows a classical “strong” interaction between Se and I (blue), but significant additional features arising from the axial hydrogens that might account for the axial orientation of the Se…I-I group.
    Click for 3D

    Click for 3D

  9. For good measure, here is the complete crystal structure search, defining any non-bonded contact between any element of group six and group seven that is <0.5Å shorter than the van del Waals contact. Our candidate is on the left hand edge of the plot.
    Se-I

References

  1. H. Maddox, and J.D. McCullough, "The Crystal and Molecular Structure of the Iodine Complex of 1-Oxa-4-selenacyclohexane, C<sub>4</sub>H<sub>8</sub>OSe.I<sub>2</sub>", Inorganic Chemistry, vol. 5, pp. 522-526, 1966. https://doi.org/10.1021/ic50038a006

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Halogen bonds: Part 1.

Saturday, November 29th, 2014

Halogen bonds are less familiar cousins to hydrogen bonds. They are defined as non-covalent interactions (NCI) between a halogen atom (X, acting as a Lewis acid, in accepting electrons) and a Lewis base D donating electrons; D….X-A vs D…H-A. They are superficially surprising, since both D and X look like electron rich species. In fact the electron distribution around X-X (A=X) is highly anisotropic, with the electron rich distribution (the “donor”)  being in a torus encircling the bond, and an electron deficient region (the “acceptor”) lying along the axis of the bond.

I will start this simple exploration of halogen bonds by a crystal structure search, defined as below, where A in the above definition is also any halogen, the donor D is a tri-alkyl nitrogen donating via a lone pair, the green contact is defined as an intermolecular distance equal to or shorter than the sum of the van der Waals radii together with an angle subtended as N…7A…7A.

halogen-search

The result of such a search is shown below:

halogen-search1
There are surprises.

  1. The sparsity of hits. If the search is repeated with A = N, O or S, only six further hits are obtained, all with A=N and X=I with one example of X=Br.
  2. There is a hot-spot at an N…I distance of 2.37Å, a massive 1.2Å shorter than the combined van der Waals radii of N and I, and with a linear N…I-I angle.

This next search replaces A with a carbon instead of a halogen. The hot-spot moves to ~2.8Å, still much shorter than the combined van der Waals radii,  and there are rather more hits this time.‡

N-IC

I will next start with a simple exploration of how the electron density on I2 changes when it accepts an electron from a donor D (ωB97XD/Def2-TZVPP-PP calculation). The following is an electron density difference isosurface (0.002au) showing how the density changes. The red phase is increased density, which adds exo to the bond, and the blue is decreased density, mostly at the iodine atom but also in the centre of the bond. These changes have axial symmetry along the axis of the I-I bond.

halogen-search1

As usual, if you want to view a 3D model of this surface, click on the graphic above.

This next difference map shows the inverse, i.e. what happens when an electron is removed from I2 to form a radical cation. Again blue shows decreased density, and this is not axially symmetric, coming from the π-system (more specifically just one of the π-MOs;  the orthogonal π-manifold actually gains red density). This is a nice way of showing that  I2  accepts electrons into the σ-manifold and looses them from the π-manifold. In other words, the density responds in a very anisotropic way to addition or loss of electrons.†

halogen-search1

In part 2, I will focus on one of the examples, HEKZOO[1] as published in 2012[2]. This is a complex between the base DABCO and molecular iodine, in which the DABCO donates electrons into that I2 σ-manifold.

‡There are only three significant hits with D=di-alkyloxygen rather than nitrogen. The first two[3],[4] involve X-A=I-I with a D…X distance of 2.8Aring; and the third X-A=Cl-Cl.

†I have now added also the density difference map for the base DABCO as a model for the donor D. Note that for this base, when an electron is lost to form the radical cation, the density reduces not just at the nitrogen lone pairs, but also the adjacent C-C bonds.

DABCO Density

This post is the first I have written since hearing the very sad news about the death of Paul Schleyer. He was a frequent commentator on these posts, and his towering presence over the last sixty years in chemistry will be sorely missed.

References

  1. Peuronen, A.., Valkonen, A.., Kortelainen, M.., Rissanen, K.., and Lahtinen, M.., "CCDC 879935: Experimental Crystal Structure Determination", 2013. https://doi.org/10.5517/ccyjn03
  2. A. Peuronen, A. Valkonen, M. Kortelainen, K. Rissanen, and M. Lahtinen, "Halogen Bonding-Based “Catch and Release”: Reversible Solid-State Entrapment of Elemental Iodine with Monoalkylated DABCO Salts", Crystal Growth & Design, vol. 12, pp. 4157-4169, 2012. https://doi.org/10.1021/cg300669t
  3. H. Bock, and S. Holl, "CCDC 147854: Experimental Crystal Structure Determination", 2001. https://doi.org/10.5517/cc4yvhd
  4. Walbaum, C.., Pantenburg, I.., and Meyer, G.., "CCDC 837899: Experimental Crystal Structure Determination", 2012. https://doi.org/10.5517/ccx3x0x

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