Posts Tagged ‘Cambridge’

Beryllocene and Uranocene: The 8, 18 and 32-electron rules.

Monday, April 25th, 2011

In discussing ferrocene in the previous post, I mentioned Irving Langmuir’s 1921 postulate that filled valence shells in what he called complete molecules would have magic numbers of 2, 8, 18 or 32 electrons (deriving from the sum of terms in 2[1+3+5+7]). The first two dominate organic chemistry of course, whilst the third is illustrated by the transition series, ferrocene being an example of such. The fourth case is very much rarer, only one example ever having been suggested[1], it deriving from the actinides. In this post, I thought I would augment ferrocene (an 18-electron example) with beryllocene (an 8-electron example) and then speculate about 32-electron metallocenes.

Cp*-beryllocene. ELF analysis. Click for 3D.

The crystal structure of (nonamethyl)bis-cyclopentadienyl beryllium [2] illustrates the octet rule directly. Be is ionised to Be2+, the charge balanced by two cyclopentadienyl anions. The octet is formally filled by donation of six electrons from one Cp* anion, and only two from the other, filling the s and p shells of the metal (the 1 and 3 in the sum alluded to earlier). The ELF analysis suggests the molecule is less ionic than ferrocene. ELF disynaptic basis are located for all five Be-C bonds on the η-5 ring, and only one for the η-1 ring. The latter basin contains 1.87 electrons (a conventional electron pair bond), whilst the five former range range from 0.57 to 0.68 electrons, adding to 5.02. The formal octet is thus not entirely filled, but in this sense, it is less ionic than ferrocene. (See DOI 10042/to-8371 for details of the calculation).

 

Uranocene is a rather different beast. The ligands are not cyclopentadienyl, but cyclo-octatetraenyl. Uranium has a radon core, and a 5f3, 6d1 and 7s2 valence shell(s) electron configuration. Ionised to U4+, formally the 5f, 6d and 7p shells are all empty; a total of 14 + 10 + 6 electrons would be required to achieve a 32-electron filled shell , or 30 additional electrons. The two COT ligands, as di-anions (achieving aromaticity) could provide only 20. So uranocene (Cambridge refcode URACEN10, DOI 10.1021/ic50111a034) is far from the holy-grail of a 32-electron complete molecule.

Uranocene. AIM analysis. Click for 3D

The QTAIM analysis of the electron density (the molecule itself is a triplet spin state) shows only six bonds from each COT ligand to the metal. The ELF analysis shows NO U-C disynaptic basins, unlike either beryllocene or ferrocene (the features surrounding the U derive from pseudopotential used for the calculation). This indicates that uranocene is the most ionic of the three metallocenes.

 

Uranocene. ELF analysis. Click for 3D

Could a molecule be contrived that might achieve (a formal) 32-electron filled 5f,6d,7p valence shell? One would probably need a ligand contributing 14 rather than 10 electrons whilst keeping the size of the ring manageable, quite a challenge. There may not be enough space for three 10-electron ligands. So, no examples of 32-electron metallocenes just yet then!

 

References

  1. J. Dognon, C. Clavaguéra, and P. Pyykkö, "Towards a 32‐Electron Principle: Pu@Pb<sub>12</sub> and Related Systems", Angewandte Chemie International Edition, vol. 46, pp. 1427-1430, 2007. https://doi.org/10.1002/anie.200604198
  2. M.M. Conejo, R. Fernández, D. del Río, E. Carmona, A. Monge, and C. Ruiz, "Synthesis and structural characterization of Be(η<sup>5</sup>-C<sub>5</sub>Me<sub>5</sub>)(η<sup>1</sup>-C<sub>5</sub>Me<sub>4</sub>H). Evidence for ring-inversion leading to Be(η<sup>5</sup>-C<sub>5</sub>Me<sub>4</sub>H)(η<sup>1</sup>-C<sub>5</sub>Me<sub>5</sub>)", Chem. Commun., pp. 2916-2917, 2002. https://doi.org/10.1039/b208972f

The Cyclol Hypothesis for protein structure: castles in the air.

Monday, April 4th, 2011

Most scientific theories emerge slowly, over decades, but others emerge fully formed virtually overnight as it were (think  Einstein in 1905). A third category is the supernova type, burning brightly for a short while, but then vanishing (almost) without trace shortly thereafter. The structure of DNA (of which I have blogged elsewhere) belongs to the second class, whilst one the brightest (and now entirely forgotten) examples of the supernova type concerns the structure of proteins. In 1936, it must have seemed a sure bet that the first person to come up with a successful theory of the origins of the (non-random) relatively rigid structure of proteins would inevitably win a Nobel prize (and of course this did happen for that other biologically important system, DNA, some 17 years later). Compelling structures for larger molecules providing reliable atom-atom distances based on crystallography were still in the future in 1936, and so structural theories contained a fair element of speculation and hopefully inspired guesswork (much as cosmological theories appear to have nowadays!).

Dorothy Wrinch was a mathematician who came up with just such a hypothesis for rigid protein structure, based in effect on elegance and symmetry, coupled with some knowledge of chemistry and crystallography[1]. She had noticed that the repeating polypeptide motif might be folded such that a cyclisation could occur to give what she termed a cyclol (an organic chemist would call this an aminol, and we would also now recognize it as a three-fold tetrahedral intermediate of the type involved in the hydrolysis of peptides). Wrinch proposed that this cyclisation could be repeated on a large scale to produce rigid scaffolds for proteins. The three-fold symmetric elegance of such motifs clearly appealed to this mathematician (the interesting symmetrical and conformational properties of the central cyclohexane-like ring were still to be fully recognised by anyone. Since Wrinch built many 3D models of her cyclols, one can but wonder how that central ring was represented, and whether its chair conformation was at all recognised. Another Nobel prize awaited the discoverer of this, Derek Barton).

The Cyclol structure. Click for 3D.

An immense controversy immediately broke out (not least because little direct spectroscopic evidence for the OH groups could be found). The story is rivetingly told by Patrick Coffey in his book Cathedrals of Science (ISBN 978-0-19-532134-0). Linus Pauling entered the fray in 1939[2], and one of the arguments he deployed was not so much symmetric elegance but thermodynamics (he also suggested hydrogen bonding and  S-S linkages for rigidifying proteins). The proposed cyclisation, he suggested, led to a very high energy species. Whilst Wrinch attempted to refute this[3], Pauling’s arguments won almost everyone over. Although Wrinch forlornly continued to promote her idea, last reviewing the topic as late as in 1963[4], crystallography was now producing cast iron data for protein structures. None have ever emerged with a cyclol motif, and this hypothesis is now firmly consigned to untaught history[5]. To this day, no examples of the tris(aminol) cyclol ring are to be found in the Cambridge small molecule crystal structure database either (although some related tetrahedral intermediates are known as crystalline species, see for example here, and they can be quite easily characterised in solution, see for example[6].

When  I read the story, it struck me that modern theory could easily verify how valid Pauling’s thermodynamic argument was. I have picked (ala)6 as my model, and have calculated the relative free energy (ΔG298) of the following three isomers.

  1. An acyclic zwitterionic form of this hexapeptide, calculated with a SCRF reaction field for water to allow for the ionic nature (ωB97XD/6-31G(d,p)), reveals a proton transfer to a neutral system, with an energy of +7.3 kcal/mol

    Acyclic (ala)6, in zwitterionic form

  2. A cyclic neutral peptide, which results from elimination of water from 1, again calculated with a water reaction field (DOI: 10042/to-8219), revealing a relative free energy of +0.0 kcal/mol

    Cyclic (ala)6

  3. The cyclic isomer 3 resulting from further cyclisation of 2 (DOI: 10042/to-8222) with a relative free energy of +69.0 kcal/mol

    Cyclol model for (ala)6.

From this, it appears that model 3 is ~69 kcal/mol less stable than the cyclic peptide 2, or 11.6 kcal/mol per amino acid residue. Pauling’s thermodynamic arguments suggested a value of ~28 kcal/mol (a value which Wrinch disputed as unreliable). So, in one sense, the above calculation is closer to Wrinch than to Pauling! In another, it still means Wrinch was wrong!! It is worth speculating why Pauling’s estimate is out. The cyclol 3 exhibits anomeric stabilizations, which of course were unknown in Pauling’s time. Both 2 and 3 exhibit attractive, but different, van der Waals attractions which contribute to their stabilities. And Pauling took no account of any entropy differences between 2 and 3. In retrospect,  3 was simply too rigid to allow most enzyme catalysis models to function, as we recognise them nowadays.

You might ask why I have revived a long forgotten theory as the topic of this post. Well, I think it is always worth revisiting the past, and re-examining old assumptions. When we do so, we find that Wrinch did not miss by as much as her detractors perhaps implied. With a little more luck, she might have gotten it right. Science is a bit like that, you need a dose of luck sometimes!

References

  1. D.M. Wrinch, "The cyclol hypothesis and the “globular” proteins", Proceedings of the Royal Society of London. Series A - Mathematical and Physical Sciences, vol. 161, pp. 505-524, 1937. https://doi.org/10.1098/rspa.1937.0159
  2. L. Pauling, and C. Niemann, "The Structure of Proteins", Journal of the American Chemical Society, vol. 61, pp. 1860-1867, 1939. https://doi.org/10.1021/ja01876a065
  3. D.M. Wrinch, "The Geometrical Attack on Protein Structure", Journal of the American Chemical Society, vol. 63, pp. 330-333, 1941. https://doi.org/10.1021/ja01847a004
  4. D. WRINCH, "Recent Advances in Cyclol Chemistry", Nature, vol. 199, pp. 564-566, 1963. https://doi.org/10.1038/199564a0
  5. C. Tanford, "How protein chemists learned about the hydrophobic factor", Protein Science, vol. 6, pp. 1358-1366, 1997. https://doi.org/10.1002/pro.5560060627
  6. H.S. Rzepa, A.M. Lobo, M.M. Marques, and S. Prabhakar, "Characterizing a tetrahedral intermediate in an acyl transfer reaction: An undergraduate 1H NMR demonstration", Journal of Chemical Education, vol. 64, pp. 725, 1987. https://doi.org/10.1021/ed064p725

From the colour blue to molecular wires

Wednesday, March 9th, 2011

In the previous post I pondered the colour of Monastral blue (copper phthalocyanine). Something did not quite fit, and so I speculated that perhaps some oxidation of the pigment might give a new species. This species (Cambridge code FEGJOQ) comprises two parts of copper phthalocyanine, 1 part of the corresponding cation, and 1 part of triodide anion. Looking at the packing of this system, I spotted something I had seen some time ago in NaI2.Acetone, namely an infinitely long and absolutely straight chain of iodine atoms, a molecular wire if you like.

An iodine molecular wire.

A different view shows how this wire runs down layers of the phthalocyanine. The iodines are 3.2Å apart, compared to the sum of their van der Waals radii of ~4.0Å.

FEGJOQ, seen edge on. Click for 3D

Four phthalocyanines stack to form a cavity for the iodine wire to run down, and the size of that cavity is perfectly filled by the iodine! One might speculate if a smaller halogen, with lots more space to rattle around it, might not form this structure!

 

End on view, showing the filling of the channel by iodines. Click for 3D

Morphing an arrow-pushing tutorial into a dihydrogen bond

Thursday, December 2nd, 2010

My university tutorial yesterday covered selective reductions of functional groups in organic chemistry. My thoughts on that topic have now morphed into something rather different. Scientific research has a habit of having this sort of thing happen.

After I completed the blog post (deliberately done whilst the memory of the tutorial was fresh on my mind), a thought then struck me. I appended a new idea to the post in the form of a comment (the actual posts themselves I feel should remain resolutely unmorphed; I tend to correct only typographical and minor errors). I had spotted that the adduct between ethanoic acid and borane had a very short H…H distance. So the obvious thing to do is to see if one might tweak the structure to further enhance the interaction. Hence below.

Acyloxy-beryllium hydride. Click for 3D

The interaction of interest is between an acidic hydrogen and the hydridic one. The former can be acidified further by employing trifluoroethanoic acid. The latter can be tweaked by replacing boron with beryllium. This newly designed molecule now exhibits a H…H distance of 1.278Å (ωB97XD/6-311G(d,p) calculation), which as these so-called dihydrogen bonds go is pretty short (H2 itself is ~0.74Å). Normal dihydrogen bonds (see for example my lecture course) are in the region of 2.0-2.2Å, although  a few crystal structures (e.g. WAGBAH in the Cambridge database) have  shorter B-H…H-O distances of around  1.76Å. A typical  H…H van der Waals distance is  ~2.4Å.  So it appears that H…H interactions can be almost continuously tuned across the whole range of short covalent, to short and medium  dihydrogen and long dispersion lengths. The AIM analysis (below), shows ρ(r) to be ~0.07 au for the bond-critical-point spanning the H…H region. Normal hydrogen bonds rarely exceed 0.04, although it’s still some way off a covalent H-H bond value (0.26).

AIM analysis.

Could the molecule above be made and characterised? Well, it is probably the case that as the H…H distance gets shorter, so the activation barrier for actually eliminating covalent H2 will get smaller and smaller. Probably, distances of  ~1.7Å represent the shortest that actually has a reasonable barrier preventing such eliminations. With the current interest in devising materials capable of storing  H2 (and absorbing/releasing it on demand), these types of molecule may perhaps prove useful. Quite a way to come starting from a tutorial on diborane reductions.

(Almost) 100 years of Lewis structures: are they still fit for purpose?

Monday, September 27th, 2010

The molecule below was characterised in 1996 (DOI: 10.1246/cl.1996.489) and given the name tris(dithiolene)vanadium (IV). No attempt was made in the original article to give this molecule a Lewis structure using Lewis electron pair bonds. This blog will explore some of the issues that arise when this is attempted.1

NAMPOG.

The name given to the molecule by the chemists who made it reflects the ligand used, which we can represent as cis-HS-CH=CH-SH (via its di-sodium salt and reaction with VCl3). Its entry in the Cambridge crystal database is NAMPOG (which carries only the slightest of semantic or structural information). The chemical name however does carry some further information, namely the designation tris implies three fold symmetry (D3h in this case), and hence that all three ligands are in fact identical (structurally).

A nominal first stab at a Lewis electron pair representation reflecting this symmetry might be as shown above. At this point we hit a logical problem with the final component of the assigned name; the formal oxidation state of the metal is designated IV. However, three moles of (-)S-CH=CH-S(-) imply the ligands carry a formal charge of 6-, and that therefore the metal must be 6+, or VI. Six however is not an oxidation state normally exhibited by vanadium. Why did the original discoverers designate it IV? Well, because careful electron counting reveals the system as a whole has 161 electrons, of which 71 are designated as valence electrons, and hence it must have one unpaired valence electron. In the representation above, that electron is shown resident on the V atom with a dot, and the ESR spectrum measured for the molecule turns out to be apparently characteristic of V(IV) systems (they do not mention whether they also compared the spectra with those derived from genuine examples of  V(II), see below). This implies (as the authors note) that a total of only 4- must be delocalized over the three dithiolene ligands.

Returning to our electron counting, of the remaining 70 valence electrons, 24 electrons are implicit above as twelve sulfur lone pairs (which are sometimes shown as double dots, but their explicit inclusion here would cause clutter) and so we presume the remaining 46 electrons must be in Lewis-like electron pair bonds. Well, the structure above implies 24 such bonds (the six C-H lines, as well as the  Hs are also omitted by convention, again to avoid clutter!). We can begin to see why the original article lacks a Lewis structure, since the one above contains too many electrons (48 rather than 46).

How might one proceed to rescue the situation? Because a great many possible Lewis structures could be drawn, we have to learn a little more about the molecule and seek recourse in the bond lengths measured for the system. The most obvious is the C-C length, which turns out to be 1.36Å, a value significantly longer than expected for a C=C double (i.e. a four electron) bond, but a little shorter than the 3-electron bond found in e.g. benzene.

A second attempt at a Lewis structure

The Lewis structure (one of three equivalent ones) now has 5 lines in the C-C region, or ~3.3 electrons per C-C bond averaged over three ligands, which seems to match the length a little better. It also has 25 lines representing nominal electron pairs and ten sulfur lone pairs, a total of 70 electrons. The net effect of this representation is to transfer two electrons from the sulfur lone pairs to the vanadium, and hence to reduce the formal charge at the metal from 6+ to 4+, or to V(IV). This sort of behaviour, where electrons can be borrowed from a ligand and used to reduce (or oxidise) the metal they are coordinated to is called non-innocent behaviour. The dithiolene ligand is notoriously non-innocent. It results in this case in our innocent assumptions that bonds are defined by an integer number of electrons [2,(3),4,(5) or 6 as in Lewis’ original classifications] are no longer adequate, and that non-integer descriptors must also be used.

There is still one counting rule we have not inspected. To complete its valence shell to reach Kr, V needs 18 valence electrons. The representation above gives it 13. So how about the following, which ends up with a valence shell of 17 electrons for vanadium (and an oxidation state of V(II))?

Third time lucky?

This implies that the V-S bonds might be a little shorter than normal. Well in NAMPOG its 2.35Å, perhaps slightly shorter than a typical V-S single bond of ~2.4Å, but in fact we are now down at the noise level, and its clear that we have probably reached (if not exceeded) the limit of semantic interpretation of the Lewis model. In this case, only three (of 100s of possible) Lewis structures have been discussed, and of course they were selected only because we had some experimental information to discriminate between them. And we must be aware that whilst Lewis structures are the simplest way of analysing the electron distribution in a molecule, far more sophisticated analyses are nowadays possible. The real question is which analysis can actually result in a greater insight into the molecule? But the least that can be said about molecule NAMPOG is that it causes one to think about the problems of representing bonding (I will draw the line however at using this example in my university admissions interviews!).

1 I thank J. P. P. (Jimmy) Stewart for drawing this molecule on my blackboard  and hence provoking this blog post.

Solid carbon dioxide: hexacoordinate carbon?

Friday, September 17th, 2010

Carbon dioxide is much in the news, not least because its atmospheric concentration is on the increase. How to sequester it and save the planet is a hot topic. Here I ponder its solid state structure, as a hint to its possible reactivity, and hence perhaps for clues as to how it might be captured. The structure was determined (DOI 10.1103/PhysRevB.65.104103) as shown below.

The structure of solid carbon dioxide. Click for 3D

The two nominal double bond distances are 1.33Å, whilst a further four O…C contacts in the shape of a square complete the coordination (2.38Å each). All would probably agree that the central carbon is best described as hexa-coordinated. This is also a hot topic. For example, note the claim made recently to have created a hexa-coordinated carbon species by design (Synthesis and Structure of a Hexacoordinate Carbon Compound, DOI: 10.1021/ja710423d) based on a motif derived from an allene:

Designed hexacoordinate carbon. Click for 3D

This claim was supported by an unusual measured property, the electron density ρ(r) and its Laplacian in the putative O…C region. These two properties are one of those (relatively rare) meetings between experiment and quantum mechanics, and their usefulness has been noted in this blog on previous occasions. However, note that in this designed structure, the O…C distances are merely 2.65-2.7Å, significantly longer than in solid carbon dioxide! So carbon dioxide, in a form many of us are familiar with (solid), can certainly be justified as being described as having a hexacoordinate carbon (although we might draw the line at describing it as having hexavalent carbon).

If oxygen atoms can approach the carbon in CO2 to within ~2.4Å, an interesting question can be posed. How close can another carbon get to CO2 without actually reacting and forming a new molecule? C-C bonds, even weak ones, are so much more interesting than C-O bonds! It would have to be a particularly nucleophilic carbon, of course. A search of the August 2010 version of the Cambridge structural database (CSD) reveals no really close approaches of another carbon to CO2. Only about 8 weak examples are found, and here the C-C distances are ~3.0-3.2Å, with the O=C=O angle in the CO2 never less than 170°. In this context, there is an intriguing and very recent report (which has not yet made it into the searchable CSD) of the structure of CO2 trapped in a cavity next to what was claimed to be a molecule of 1,3-dimethyl cyclobutadiene, or CBD (see 10.1126/science.1188002 and the discussion of this article in my earlier blog post). The focus in that report was on the “Mona Lisa of organic chemistry”, namely the CBD unit. One feels that the structure of the adjacent CO2 was of lesser interest to the authors. According to a visual image of this system, the CBD and CO2 pair show quite an intimate approach via their carbon atoms (a ghostly C-C bond is clearly represented). This raises the interesting question of whether the description of this pair should be of two intimate but nevertheless separate and relatively unperturbed molecules not connected by a covalent bond (“more indicative of a strong van der Waals contact than of covalent bonding“) or of a pair fully bound by a covalent C-C bond between them?

The issue of what is an interaction, and what is a bond continues to raise its often controversial head. And quantum theory continues to provide a multitude of interpretations as well.

Uncompressed Monovalent Helium

Saturday, October 3rd, 2009

Quite a few threads have developed in this series of posts, and following each leads in rather different directions. In this previous post the comment was made that coordinating a carbon dication to the face of a cyclopentadienyl anion resulted in a monocation which had a remarkably high proton affinity. So it is a simple progression to ask whether these systems may in turn harbour a large affinity for binding not so much a H+ as the next homologue He2+?

Inventing the  Helium bond

Inventing the Helium bond

This possibility is explored with the series X=Be, B, C (tetramethyl substituted, resulting in neutral, +1 and +2 systems overall). The first two emerge as stable in terms of having all positive force constants for C4v symmetry; the last emerges as a transition state and is not discussed further. The specific system X=B has a B-He bond length of 1.317Å/B3LYP/6-311G(d,p), 1.305Å/B3LYP/Def2-QZVPP and 1.290Å/double-hybrid RI-B2GP-B2PLYP/TZVPP, which does seem as if it might be typical of a single bond between these two elements. The ρ(r)B-He AIM value (B3LYP/6-311G(d,p) is 0.069 au, and νB-He of 713 cm-1 (727 for Def2-QZVPP basis) makes it about one third the strength of a C-H bond. The disynaptic basin for the B-He region integrates to 1.99 electrons, whilst the four B-C basins correspond to 1.22 electrons each.

X Charge ρ(r) X-He C-B ELF
integration
νX-He, cm-1 Repository
Be 0 0.031 1.10 484 10042/to-2443
B 1 0.069 1.22 713 10042/to-2444

10042/to-2446

10042/to-2453

C 2 0.026 136 10042/to-2445
AIM for X=B-He

AIM for X=B-He. Click for 3D

B-He vibrational stretching mode

B-He stretching mode. Click to vibrate

We can conclude that for X=B, this species exhibits not only a pentavalent boron atom, but a monovalent helium atom. The latter bond may indeed be amongst the strongest ever proposed for this element in a ground state, and indeed perhaps is even viable as a solid crystalline compound rather than merely existing in the gas phase. The Cambridge crystal database contains no entries for He or Ne, not even as an encapsulated clathrate (although crystal structures of such complexes for Kr and Ar are known). Theoretical studies of the rare gases in endohedral fullerene-like cages (DOI: 10.1002/chem.200801399) predict that under these compressed circumstances e.g. two helium atoms can approach each other to 1.265Å or less (see also DOI: 10.1002/chem.200700467) but these close approaches were not considered to be chemical bonds as we think of them. Perhaps Merino, Frenking, Krapp and co’s search for the chemistry of helium (they had found it earlier in the gas phase excited states of their molecules, DOI: 10.1021/ja00254a005) might be realised for the ground state of the system described here.