Posts Tagged ‘Carbon’

Tetrahedral carbon and cyclohexane.

Wednesday, August 22nd, 2018

Following the general recognition of carbon as being tetrahedrally tetravalent in 1869 (Paterno) and 1874 (Van’t Hoff and Le Bell), an early seminal exploitation of this to the conformation of cyclohexane was by Hermann Sachse in 1890.[1] This was verified when the Braggs in 1913[2], followed by an oft-cited article by Mohr in 1918,[3] established the crystal structure of diamond as comprising repeating rings in the chair conformation.† So by 1926, you might imagine that the shape (or conformation as we would now call it) of cyclohexane would be well-known. No quite so for everyone!

When The Journal of the Imperial College Chemical Society (Volume 6) was brought to my attention, I found an article by R. F Hunter;

He proceeds to argue as follows:

  1. The natural angle subtended at a tetrahedral carbon is 109.47°.
  2. “The internal angle between the carbon to carbon valencies of a six-membered ring cyclohexane will, if the ring is uniplanar, be … 120°.
  3. “When the cyclohexane ring is prepared … we must therefore have the pushing apart of two of the valencies”.
  4. The object of the experiments commenced in this College in 1914 was “to find what effect the pushing apart of the valencies …must have on the angle between the remaining pair of valencies“.
  5. You do wonder then why the assumption highlighted in red above was never really questioned during the twelve-year period of investigating angles around tetrahedral carbon.

The article itself is quite long, reporting the synthesis of many compounds in search of the postulated effect. Of course around twenty years later, Derek Barton used the by then generally accepted conformation of cyclohexane to explain reactivity in what become known as the theory of conformational analysis.

These two articles dating from 1926, and probably thought lost to science, show how some ideas can take decades to have any influence, whilst others can take root very much more quickly.

†The chair cyclohexane structure is easily discerned from Figure 7 in the Braggs’ paper![2]

References

  1. H. Sachse, "Ueber die geometrischen Isomerien der Hexamethylenderivate", Berichte der deutschen chemischen Gesellschaft, vol. 23, pp. 1363-1370, 1890. https://doi.org/10.1002/cber.189002301216
  2. W.H. Bragg, and W.L. Bragg, "The structure of the diamond", Proceedings of the Royal Society of London. Series A, Containing Papers of a Mathematical and Physical Character, vol. 89, pp. 277-291, 1913. https://doi.org/10.1098/rspa.1913.0084
  3. E. Mohr, "Die Baeyersche Spannungstheorie und die Struktur des Diamanten", Journal für Praktische Chemie, vol. 98, pp. 315-353, 1918. https://doi.org/10.1002/prac.19180980123

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How does carbon dioxide coordinate to a metal?

Saturday, May 6th, 2017

Mention carbon dioxide (CO2) to most chemists and its properties as a metal ligand are not the first aspect that springs to mind. Here thought I might take a look at how it might act as such.

There are up to five binding modes with one metal that one might envisage:

  1. Bonded interaction with the metal via just one oxygen atom,
  2. Bonded interaction via just the central carbon atom,
  3. Bonded interaction via the π-face of one C=O double bond,
  4. A weaker non-bonded interaction via carbon, or
  5. via oxygen.

Search queries of the Cambridge structure database (CSD) for these five modes are illustrated below (dataDOI: 10.14469/hpc/2524), with the constraints being applied to how many bonds (of unspecified type) each atom carries, along with no disorder and no errors. Thus query 1 is constrained by 1-coordination on one oxygen, and two on the carbon and other oxygen. 

  1. This query yields four hits: 10.5517/ccvcdq9, 10.5517/cc12nq6n, 10.5517/cc12nq5m, 10.5517/cc12nq4l. The angle subtended at the central carbon of the CO2 ranges from 172-176°, a very modest bending of the linear CO2. There are no examples where the metal is bonded to both oxygens.
  2. The next category involves the metal binding just to the central carbon. Two examples are known, differentiated from O-coordination by a more acute angle at the central carbon of 121-132°.
  3. The π-coordinated type requires a slightly more complex search query, shown below. The π-complex is defined as adding one coordination to each of one oxygen and the carbon. 

    This reveals 16 examples:

    The sine of the angle subtended at the centroid of one C-O bond shows that for most of the examples, the metal is close to perpendicular to this bond. The angle subtended at the central carbon ranges from 128-138, rather larger than the examples where the metal is bound just to the carbon. I have picked these two for illustration. The first (dataDOI: 10.5517/cc86r17) contains both CO2 and CO coordinated to the metal.This one (dataDOI: 10.1021/ic101652e) contains a short metal-centroid distance of 1.78Å (as also does 10.5517/ccz34kr). 

    There are two examples where BOTH π-CO bonds are coordinated to a metal; 10.5517/ccqlv7c and 10.5517/ccqlv8d (Ni-centroid distance 1.9Å) but these are intriguing because the two π-complexes are co-planar and not orthogonal.

  4. The final two cases are defined in the CSD database by having not so much bonds between metal and either C or O, as close intermolecular contacts typical of e.g. hydrogen bonds. This one (dataDOI: 10.5517/cc12nq9r) is to Fe, with a metal-C distance of 2.87Å which is significantly shorter than the anticipated sum of the van der Waals radii of the two atoms. The next (dataDOI: 10.5517/cc12npn2) has a close approach of Co to O of 2.23Å. The angles subtended at the carbon range from 174-180°. There are no convincing examples of close non-bonded approaches of the metal to both oxygen atoms simultaneously.

It is striking that the searches (as defined above) reveal relatively few examples. This might simply be a result of how the compounds are indexed in the CSD, reflected in the coordination constraints applied in the searches. Nevertheless, we see three quite different types of ligand-metal coordination in which bonds can be said to form and a more diffuse spectrum of weaker interactions to carbon dioxide. As a metal ligand, it is certainly interesting! Several deserve their wavefunctions looked at and I might report back on this aspect.

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The π-π stacking of aromatic rings: what is their closest parallel approach?

Thursday, April 13th, 2017

Layer stacking in structures such as graphite is well-studied. The separation between the π-π planes is ~3.35Å, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7Å). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen bonding can contract the vdW distance sum by up to ~0.8Å or even more? This question was prompted by the separation calculated for the ion-pair cyclopropenium cyclopentadienide (~2.6-2.8Å).

The search query for the Cambridge structure database is shown below.


The query (dataDOI: 10.14469/hpc/2471) defines centroids for two benzenoid rings, both comprising only 3-coordinated carbons. The sine of an angle subtended at each centroid to the other and to one ring carbon attempts to track how parallel the two rings are (strictly speaking, 12 such angles should be included). If the sines of both angles are 1.00, then the two centroids overlap orthogonally. A search constrained to no disorder, no errors and R < 0.05 reveals 1107 hits at a centroid-centroid distance of < 3.5Å. The colour code (red) indicates the distances in the range 3.4-3.5Å, which matches that of graphite, while distances down to 3.2Å (yellow-green) are not uncommon. 

Here is another way of representing these results, in which the centroid-centroid distances (measured from the positions of 12 carbon atoms and hence statistically more reliable than any individual atom pair distance) are multiplied by either sin(ANGa) or sin(ANGb). The number of occurrences with distances < 3.2Å is less than 32 (out of 1107).

Taking a look at some of these outliers, PAZJEG has two entries, one with a short distance (dataDOI: 10.5517/ccsffzl) and one with a normal distance[1], which does tend to cast doubt on the former.

ZOMSEB[2], DataDOI: 10.5517/CCZS2MF) appears to have the planes of the molecules stacked ~2.5Å apart.

OXUDES02[cite10.1016/j.poly.2016.09.046[/cite], DataDOI: 10.5517/CCDC.CSD.CC1MBBFQ) has a separation of ~2.6Å.

Verifying these and other outliers would require expert inspection of the crystallographic data and its refinement. This might require access to the hkl  structure factors, data which are now being “strongly encouraged”‡ for deposition with the CSD, but which are not present for most structures deposited before ~2016. In extreme cases, the original diffraction images collected by the cameras would allow for a fully independent re-analysis, data which however is rarely if ever deposited.

So the separation of π-π stacked six-membered benzenoid rings is only infrequently less than ~3.2Å in measured crystal structures. There are hints it might reach as short as ~2.6Å, but  such examples with values significantly less than 3.2Å do require expert validation before they can be called real. 

‡See structuredepositioninformation/ “We strongly encourage data to be deposited either with imbedded structure factor data or with an associated FCF or HKL structure factor file.”

References

  1. J. Rogan, D. Poleti, and L. Karanović, "Synthesis, Structure, and Thermal Properties of Two New Inorganic‐organic Framework Compounds: Hexaaqua(<i>μ</i><sub>2</sub>‐1,2,4,5‐benzenetetracarboxylato)‐bis(<i>N</i>,<i>N′</i>‐1,10‐phenathroline)dicobalt(II) Dihydrate and Hexaaqua(<i>μ</i><sub>2</sub>‐1,2,4,5‐benzenetetracarboxylato)‐bis(<i>N</i>,<i>N′</i>‐2,2′‐dipyridylamine)dinickel(II) Tetrahydrate", Zeitschrift für anorganische und allgemeine Chemie, vol. 632, pp. 133-139, 2005. https://doi.org/10.1002/zaac.200500292
  2. P. Das, C.K. Jain, S.K. Dey, R. Saha, A.D. Chowdhury, S. Roychoudhury, S. Kumar, H.K. Majumder, and S. Das, "Synthesis, crystal structure, DNA interaction and in vitro anticancer activity of a Cu(<scp>ii</scp>) complex of purpurin: dual poison for human DNA topoisomerase I and II", RSC Adv., vol. 4, pp. 59344-59357, 2014. https://doi.org/10.1039/c4ra07127a

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Supporting information: chemical graveyard or invaluable resource for chemical structures.

Friday, March 31st, 2017

Nowadays, data supporting most publications relating to the synthesis of organic compounds is more likely than not to be found in associated “supporting information” rather than the (often page limited) article itself. For example, this article[1] has an SI which is paginated at 907; almost a mini-database in its own right! Here I ponder whether such dissemination of data is FAIR (Findable, accessible, interoperable and re-usable).[2]

I am going to use this article as my starting point.[3] One of the compounds discussed there is shown below; it is not explicitly discussed in the main body of the article. So how findable is it?

  1. A search of Scifinder (Chemical abstracts) using the structure above reveals one hit, the source being the expected one.[3]
  2. A search of Reaxys (used to be Beilstein) reveals no hits in their own database, but one hit is noted in …
  3. Pubchem, where it occurs as substance 163835830. The source is again cited correctly[3]. One of the properties reported is the InChI key: JSLVVAICXSKSEQ-UHFFFAOYSA-N. This is the same key generated from the structure drawing programs Chemdraw or ChemDoodle.
  4. Google on the other hand finds nothing for JSLVVAICXSKSEQ-UHFFFAOYSA-N.[4]
  5. I also tried Google Scholar but again with no luck.

So supporting information does appear to be indexed by both Chemical Abstracts and Pubchem; it is thankfully not a graveyard![5] The chemical databases do return valuable additional information about the molecule, such as e.g. its InChI key and much else besides. Given that presumably the open PubChem resource IS indexed by Google, it must be a policy somewhere that prevents e.g. JSLVVAICXSKSEQ-UHFFFAOYSA-N from being found.

I suppose the next question might be Supporting information: chemical graveyard or invaluable resource for chemical spectra? I confess here that this post was in fact inspired by a previous one on the topic of the provenance of NMR spectra. And perhaps also with some input from the concept of sonification of spectra, in which an instrumental spectrum is converted into a sound signature to allow blind people access to such information.‡ I wonder whether a sonified unique digital signature could be used to search for spectra, somewhat in the manner that InChI helped in tracking down (or not) the molecule above? I think it would be reasonable to say that e.g. NMR spectra as embedded in say a 907 page supporting information document are likely to be very much less FAIR[2]. The solution there of course is better provenance and better metadata, as I previously mulled.

‡I cannot help but wonder what a carbonyl group sounds like!

References

  1. J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", Journal of the American Chemical Society, vol. 139, pp. 3209-3226, 2017. https://doi.org/10.1021/jacs.6b13229
  2. M.D. Wilkinson, M. Dumontier, I.J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. Boiten, L.B. da Silva Santos, P.E. Bourne, J. Bouwman, A.J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C.T. Evelo, R. Finkers, A. Gonzalez-Beltran, A.J. Gray, P. Groth, C. Goble, J.S. Grethe, J. Heringa, P.A. ’t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S.J. Lusher, M.E. Martone, A. Mons, A.L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M.A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, and B. Mons, "The FAIR Guiding Principles for scientific data management and stewardship", Scientific Data, vol. 3, 2016. https://doi.org/10.1038/sdata.2016.18
  3. G.M.S. Yip, Z. Chen, C.J. Edge, E.H. Smith, R. Dickinson, E. Hohenester, R.R. Townsend, K. Fuchs, W. Sieghart, A.S. Evers, and N.P. Franks, "A propofol binding site on mammalian GABAA receptors identified by photolabeling", Nature Chemical Biology, vol. 9, pp. 715-720, 2013. https://doi.org/10.1038/nchembio.1340
  4. S.J. Coles, N.E. Day, P. Murray-Rust, H.S. Rzepa, and Y. Zhang, "Enhancement of the chemical semantic web through the use of InChI identifiers", Organic & Biomolecular Chemistry, vol. 3, pp. 1832, 2005. https://doi.org/10.1039/b502828k
  5. M. Karthikeyan, and R. Vyas, "ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files", Journal of Cheminformatics, vol. 8, 2016. https://doi.org/10.1186/s13321-016-0175-x

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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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Posted in Chemical IT, crystal_structure_mining, Interesting chemistry | 1 Comment »

Allotropic halogens.

Sunday, April 26th, 2015

Allotropes are differing structural forms of the elements. The best known example is that of carbon, which comes as diamond and graphite, along with the relatively recently discovered fullerenes and now graphenes. Here I ponder whether any of the halogens can have allotropes.

Firstly, I am not aware of much discussion on the topic. But ClF3 is certainly well-known, and so it is trivial to suggest BrBr3, i.e. Br4 as an example of a halogen allotrope. Scifinder for example gives no literature hits on such a substance (either real or as a calculation; it is not always easy nowadays to tell which). So, is it stable? A B3LYP+D3/6-311++G(2d,2p) calculation reveals a free energy barrier of 17.2 kcal/mol preventing Br4 from dissociating to 2Br2.[1] The reaction however is rather exoenergic, and so to stand any chance of observing Br4, one would probably have to create it at a low temperature. But say -78° would probably be low enough to give it a long lifetime; perhaps even 0°.

Br4c
Br4

So how to make it? This is pure speculation, but the red colour of bromine originates from (weak, symmetry forbidden) transitions, with energies calculated (for the 2Br2 complex) as 504, 492nm. Geometry optimisation of the first singlet excited state of 2Br2 produces the structure below, not that different from Br4.
2Br2-excited

 

At least from these relatively simple calculations, it does seem as if an allotrope of bromine might be detectable spectroscopically, if not actually isolated as a pure substance.

References

  1. H.S. Rzepa, "Br4", 2015. https://doi.org/10.14469/ch/191228

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