Henry Rzepa's blog

Here is another selection from the Molecules-of-the-Year shortlist published by C&E News, in which hexagonal planar transition metal coordination is identified. This was a mode of metal coordination first mooted more than 100 years ago,[1] but with the first examples only being discovered recently. The C&E News example comprises a central palladium atom surrounded by three hydride and three magnesium atoms, all seven atoms being in the same plane.

As the original article makes clear,[1] the relative orbital simplicity of these early main group based ligands allows the bonding to be better understood, hence itself allowing “additional design principles” to be introduced for transition metal complexes. Here I thought I might extend the scope of this motif by a generalised crystal search for any other hexagonal planar structures to be found in the Cambridge crystal structure database.

A search query can be constructed by defining a plane using the six ligand atoms and then constraining the perpendicular distance between this plane and the transition metal atom at the centre to < 0.1Å. Six angles between adjacent ligands are then themselves constrained to the range 0-70° and the coordination of the central atom can also be constrained to either 6, 7 or 8. All searches are also defined by no disorder and no errors. The search queries can be found at DOI: 10.14469/hpc/6731

I carried out a number of separate searches. The least constrained (any coordination number at the central atom, and any type of attached ligand atom) produced 62 hits, exhibiting a variety of sometimes complex coordination modes. To simplify the search, I separated the searches into specific types. You can view 3D models of any of the molecules below by clicking on the static image.

1. The first restricted the transition metal atom to 6-coordinate and for which the ligands all derive from the early main group periods (1A, 2A and H). The sole example (NORLOY[[1], DOI: 10.5517/ccdc.csd.cc2235v7) is the one noted above.
2. The next search restricted all the ligands to a transition metal connected to the central atom, along with 6-coordination. Again just one hit (RISQEP[2] dating from 1997 and comprising a central Au atom surrounded by four Au-based ligands and two Fe-based ligands. This type of molecule is a member of a class known as a hexagonal planar metal cluster.

   

3. This search now constrains all six ligands as comprising late main group atoms bonding to the central metal. Two hits, VOVZOV, dating from 1992[3] with a P-based ligand Ni central atom and ZUDWUQ from 1996[4] using As and Ni.

   

4. The next category combines the previous two, with ligands either from the transition series or the late main group series, resulting in four more hits (HACBOF and HACBUL[5] (DOI: 10.5517/ccdc.csd.cc1n26pm and 10.5517/ccdc.csd.cc1n26qn) using a combination of three carbons (as acetylide)  and three Ag ligands, with Cu as the central ligand.

   

5. Next, any ligand is allowed, together with a 7-coordinate central atom. Three examples, including  VAPZEU (2016, [6], DOI: 10.5517/ccdc.csd.cc1md045) with three Pd and three Si hexagonal ligands, with an additional 7th Cu surrounding a central Pd.

    

6. One example (of eight found) with 8-coordination at central atom (1996, NANPOH[7]), a central Cd, six oxygen ligands and two further cyanide axial ligands.

   

7. To finish, a rather wacky polymeric example with Ti at the centre, six hydrogens deriving from a terminal borane as the hexacoordinate planar motif and two axial P ligands (PEDJOY[8], DOI: 10.5517/ccb0d6x).

   

I hope this short journey through hexacoordinate planar transition metal complexes has revealed at least a flavour of the diversity in this category. I am also going to take some gentle issue with the C&E News reporting of this molecule, “Scientists proposed a hexagonal planar geometry more than 100 years ago, but it has never been captured in crystal form until now” (referring to the 2019 article which inspired this blog[1]). As I hope I have shown, a number of the examples above in crystal form actually emerged rather earlier than 2019!

References

1. M. Garçon, C. Bakewell, G.A. Sackman, A.J.P. White, R.I. Cooper, A.J. Edwards, and M.R. Crimmin, "A hexagonal planar transition-metal complex", Nature, vol. 574, pp. 390-393, 2019. https://doi.org/10.1038/s41586-019-1616-2
2. V.G. Albano, M.C. Iapalucci, G. Longoni, L. Manzi, and M. Monari, "Synthesis of [Au₃Fe₂(CO)₈(dppm)]^- and [Au₅Fe₂(CO)₈(dppm)₂]⁺:  X-ray Structures of [NEt₄][Au₃Fe₂(CO)₈(dppm)] and [Au₅Fe₂(CO)₈(dppm)₂][BF₄]", Organometallics, vol. 16, pp. 497-499, 1997. https://doi.org/10.1021/om960850g
3. R. Ahlrichs, D. Fenske, H. Oesen, and U. Schneider, "Synthesis and Structure of [Ni(P<i>t</i>Bu₆)] and [Ni₅(P<i>t</i>Bu)₆(CO)₅] and Calculations on the Electronic Structure of [Ni(P<i>t</i>Bu)₆] and (PR)₆, R = <i>t</i>Bu,Me", Angewandte Chemie International Edition in English, vol. 31, pp. 323-326, 1992. https://doi.org/10.1002/anie.199203231
4. E. Hey‐Hawkins, M. Pink, H. Oesen, and D. Fenske, "Synthesen und Charakterisierung von [Ni(<i>t</i>BuAs)₆] und [Pd(<i>t</i>BuAs)₆]", Zeitschrift für anorganische und allgemeine Chemie, vol. 622, pp. 689-691, 1996. https://doi.org/10.1002/zaac.19966220420
5. S.C.K. Hau, M.C. Yeung, V.W. Yam, and T.C.W. Mak, "Assembly of Heterometallic Silver(I)–Copper(I) Alkyl-1,3-diynyl Clusters via Inner-Core Expansion", Journal of the American Chemical Society, vol. 138, pp. 13732-13739, 2016. https://doi.org/10.1021/jacs.6b08674
6. M. Tanabe, R. Yumoto, T. Yamada, T. Fukuta, T. Hoshino, K. Osakada, and T. Tanase, "Planar PtPd₃ Complexes Stabilized by Three Bridging Silylene Ligands", Chemistry – A European Journal, vol. 23, pp. 1386-1392, 2016. https://doi.org/10.1002/chem.201604502
7. J. Kim, and K. Kim, "NEW THREE DIMENSIONAL [Cd(CN)₂]_n FRAMEWORK FORMED WITH CADMIUM CYANIDE AND Cd(CN)₂·(18-CROWN-6): CRYSTAL STRUCTURE OF [Cd(CN)₂]·1/2[Cd(CN)₂ (18-CROWN-6)]·3/2EtOH⁺", Journal of Coordination Chemistry, vol. 37, pp. 7-15, 1996. https://doi.org/10.1080/00958979608023536
8. D.M. Goedde, and G.S. Girolami, "Titanium(II) and Titanium(III) Tetrahydroborates. Crystal Structures of [Li(Et₂O)₂][Ti₂(BH₄)₅(PMe₂Ph)₄], Ti(BH₄)₃(PMe₂Ph)₂, and Ti(BH₄)₃(PEt₃)₂", Inorganic Chemistry, vol. 45, pp. 1380-1388, 2006. https://doi.org/10.1021/ic051556w

I have previously looked at the topic of hydrogen bonding interactions from the hydrogen of chloroform Here I generalize C-H…O interactions by conducting searches of the CSD (Cambridge structure database) as a function of the carbon hybridisation. I am going to jump straight to a specific molecule XEVJIR (DOI: 10.5517/cc5fgpq) identified from the searches appended to this post as interesting for further inspection.[1]

The distances from the carbonyl oxygen to CH groups of an adjacent intermolecular molecule are shown, revealing a bifurcated strong + weaker CH…O interaction. I would note that the CH…O distances are un-normalized, in the sense that a C-H distance obtained from X-ray diffraction data is normally about 0.1Å too short. A corrected value for the H…O distance is probably closer to 1.994Å. Next, a B3LYP+G3BJ/Def2-TZVPP calculation of just this dimeric interaction, which shows a somewhat different pattern, particularly from the carbonyl to the sp³-C-H (FAIR data DOI: 10.14469/hpc/5943) with one distance being shorter and one longer.

Click to load 3D model

A QTAIM analysis reveals the electron density ρ(r) of 0.021au, a relatively high value indicating a relatively strong interaction.

Side-views reveals a possible reason for why the calculation does not match the crystal structure. In the crystal structure, the sp³-CH₂ group adopts a different conformation from that computed for just two interacting molecules, since this shape allows more efficient stacking of layers and hence allowing stabilizing dispersion energy between the layers to overcome some loss of hydrogen bonding energies in the plane of the layer. If this packing constraint is removed in the pure dimer, one sp³-CH moves into the plane allowing a shorter interaction to the carbonyl oxygen and the other sp³-CH adopts a pure axial position, unconstrained by any packed layer above it.The absence of layered dispersion attractions is hence compensated by forming strong CH…O interactions.

A calculation using six molecules arranged in three layers of two is an attempt to add back at least some of the layering dispersion terms (a full periodic boundary lattice calculation is the proper way of doing this calculation, but at the level chosen here would take far too much computer time!). The new CH…O distances are now 2.018 and 2.384Å (compared to 2.036 and 2.199Å for a model with just two molecules). Probably, more layers would be needed to replicate the crystal structure more accurately.

And now for the searches. The first is for sp-hybridised carbon, as an intermolecular interaction (R < 0.05, no errors, no disorder, T=<150K, H-position normalised for distances shorter than the sum of the vdW radii -0.4), for which a clear hot spot occurs at a H…O distance of ~2.1Å

Intermolecular to sp carbon

Next, sp²-C as an intermolecular interaction (T=<90K), where the hot spot is less distinct, being at the distance cut-off specified for the search. The shortest distance is ~2.0Å. I will return to this example shortly.

Intermolecular to sp2 carbon

An intramolecular version of this search shows a clearer hotspot, again at ~2.15Å

Intramolecular to sp2 carbon

Next, intramolecular sp³ hybridisation, for which there few examples with no clear hotspot.

Intramolecular to sp3 carbon

Finally, intermolecular sp³ hybridisation. The H…O distance hotspot is very slightly longer, as might be expected for a less acidic hydrogen. Nonetheless, the variation in the H…O distances with hybridisation is perhaps unexpectedly small.

To summarise, by performing a general search of the crystal structure database, one can identify general trends and then go to inspect outliers. In this case, this brought the focus onto an (dare I say otherwise umremarkable) molecule in which layers of aromatic molecules set up a competition between intra-layer CH…O hydrogen bonding and inter-layer dispersion stabilizations. I suspect this competition between these two type of weak interactions is far more common than is generally recognised.

References

1. K.S. Huang, M.J. Haddadin, M.M. Olmstead, and M.J. Kurth, "Synthesis and Reactions of Some Heterocyclic Azacyanines¹", The Journal of Organic Chemistry, vol. 66, pp. 1310-1315, 2001. https://doi.org/10.1021/jo001484k

In the previous post, I noted the crystallographic detection of an unusually short non-bonded H…H contact of ~1.5Å, some 0.9Å shorter than twice the van der Waals radius of hydrogen (1.2Å, although some sources quote 1.1Å which would make the contraction ~0.7Å). This was attributed to dispersion attractions accumulating in the rest of the molecule. I asked myself what the potential might be for other elements to reveal significantly contracted non-bonded distances as a result of dispersive attractions.

Here is a simple search of the CSD (Cambridge structure database, query DOI: 10.14469/hpc/2700) for the monovalent halogens as in C-X. The other constraints are R<0.05, no errors, no disorder, normalised hydrogen positions and a non-bonded intermolecular contacts ≥0.4Å shorter than the sum of the van der Waals radii (a recent compendium of atomic values is available here[1]). I should state at the outset that this sort of search for non-bonded contacts is quite effective at revealing errors in the crystallographic determination, despite the search request that there be none. None, that is, that have been identified; there are many that have not been! So this survey only aims to tease out any broad trends, rather than a specific focus on individual systems.

Hits	Comments
15,500	H…H, vdW sum = 2.4Å; The accepted shortest H…H contacts are around 1.5Å; it is likely the majority of entries (all?) with shorter values are crystallographic errors. There is a curious maximum at ~1.78Å which probably relates to the H…H non-bonded distance in CH2 groups, despite the attempted constraint that the interaction be intermolecular.
31	F…F, vdW sum = 2.94Å; there are few examples in total and even fewer with the non-bonded distance contracted by ≥0.5Å. Those with ≥0.8Å are probably crystal errors.
70	Cl…Cl vdW sum =3.5Å. Examples at distances of <2.0Å (a contraction of 1.5Å) are almost certainly errors, even the contractions ~1.0Å are suspect. Does this however indicate Cl is more polarisable than F?
26	Br…Br vdW sum = 3.7Å. Examples contracted by ≥0.4Å are isolated (errors?).
10	I…I vdW sum = 3.96Å. There are no examples contracted by ≥0.5Å; shorter contractions are again errors?
1164	H…F vdW sum = 2.67Å. The separator between real values and probable errors is ~2.1Å, which indicates contractions of  0.6Å are probably real.
222	H…Cl vdW sum = 2.95Å. The separator between real values and probable errors is ~2.4Å; contractions of  ~0.5Å are probably real.
37	H…Br vdW sum = 3.05Å. The separator between real values and probable errors is ~2.8Å; contractions of  ~0.3Å are probably real.
4	H…I vdW sum = 3.18Å. More data is needed!

We see from these results that the number of short H…H contacts far exceeds those found for the halogen series.^‡ Clearly whilst the electron density surrounding H is low, that for the halogens is far higher and hence that electron repulsions are going to be far greater. The effect is attenuated if one partner is H itself, with van der Waals contractions in-between those for X…X  and H…H contacts.

This brief survey suggests that  H…H distances are by far the best for probing close contacts brought about by dispersion attractions. Perhaps the next element to focus on for such effects might be chlorine rather than fluorine. For example, see DOI: 10.5517/cczjyhx, being Ph₃C-Cl…Cl-CPh₃ where the Cl…Cl distance is contracted by ~0.3Å. What would happen if the Ph groups were adorned with t-butyl groups to increase the dispersion attractions?

^‡ It might of course also mean that the van der Waals radius for H is set too high.

References

1. S. Alvarez, "A cartography of the van der Waals territories", Dalton Transactions, vol. 42, pp. 8617, 2013. https://doi.org/10.1039/c3dt50599e

In the previous post, I noted the crystallographic detection of an unusually short non-bonded H…H contact of ~1.5Å, some 0.9Å shorter than twice the van der Waals radius of hydrogen (1.2Å, although some sources quote 1.1Å which would make the contraction ~0.7Å). This was attributed to dispersion attractions accumulating in the rest of the molecule. I asked myself what the potential might be for other elements to reveal significantly contracted non-bonded distances as a result of dispersive attractions.

Here is a simple search of the CSD (Cambridge structure database, query DOI: 10.14469/hpc/2700) for the monovalent halogens as in C-X. The other constraints are R<0.05, no errors, no disorder, normalised hydrogen positions and a non-bonded intermolecular contacts ≥0.4Å shorter than the sum of the van der Waals radii (a recent compendium of atomic values is available here[1]). I should state at the outset that this sort of search for non-bonded contacts is quite effective at revealing errors in the crystallographic determination, despite the search request that there be none. None, that is, that have been identified; there are many that have not been! So this survey only aims to tease out any broad trends, rather than a specific focus on individual systems.

Hits	Comments
15,500	H…H, vdW sum = 2.4Å; The accepted shortest H…H contacts are around 1.5Å; it is likely the majority of entries (all?) with shorter values are crystallographic errors. There is a curious maximum at ~1.78Å which probably relates to the H…H non-bonded distance in CH2 groups, despite the attempted constraint that the interaction be intermolecular.
31	F…F, vdW sum = 2.94Å; there are few examples in total and even fewer with the non-bonded distance contracted by ≥0.5Å. Those with ≥0.8Å are probably crystal errors.
70	Cl…Cl vdW sum =3.5Å. Examples at distances of <2.0Å (a contraction of 1.5Å) are almost certainly errors, even the contractions ~1.0Å are suspect. Does this however indicate Cl is more polarisable than F?
26	Br…Br vdW sum = 3.7Å. Examples contracted by ≥0.4Å are isolated (errors?).
10	I…I vdW sum = 3.96Å. There are no examples contracted by ≥0.5Å; shorter contractions are again errors?
1164	H…F vdW sum = 2.67Å. The separator between real values and probable errors is ~2.1Å, which indicates contractions of  0.6Å are probably real.
222	H…Cl vdW sum = 2.95Å. The separator between real values and probable errors is ~2.4Å; contractions of  ~0.5Å are probably real.
37	H…Br vdW sum = 3.05Å. The separator between real values and probable errors is ~2.8Å; contractions of  ~0.3Å are probably real.
4	H…I vdW sum = 3.18Å. More data is needed!

We see from these results that the number of short H…H contacts far exceeds those found for the halogen series.^‡ Clearly whilst the electron density surrounding H is low, that for the halogens is far higher and hence that electron repulsions are going to be far greater. The effect is attenuated if one partner is H itself, with van der Waals contractions in-between those for X…X  and H…H contacts.

This brief survey suggests that  H…H distances are by far the best for probing close contacts brought about by dispersion attractions. Perhaps the next element to focus on for such effects might be chlorine rather than fluorine. For example, see DOI: 10.5517/cczjyhx, being Ph₃C-Cl…Cl-CPh₃ where the Cl…Cl distance is contracted by ~0.3Å. What would happen if the Ph groups were adorned with t-butyl groups to increase the dispersion attractions?

^‡ It might of course also mean that the van der Waals radius for H is set too high.

References

1. S. Alvarez, "A cartography of the van der Waals territories", Dalton Transactions, vol. 42, pp. 8617, 2013. https://doi.org/10.1039/c3dt50599e