Posts Tagged ‘pence’

Aromatic electrophilic substitution. A different light on the bromination of benzene.

Wednesday, March 12th, 2014

My previous post related to the aromatic electrophilic substitution of benzene using as electrophile phenyl diazonium chloride. Another prototypical reaction, and again one where benzene is too inactive for the reaction to occur easily, is the catalyst-free bromination of benzene to give bromobenzene and HBr. 

br2+benzenebr2+benzene

The “text-book” mechanism involves nucleophilic attack by the benzene on the bromine to form a “Wheland intermediate” (the blue arrows) followed in a clear second step by proton removal by the liberated bromide anion (the red arrows). But one group had other ideas[1], proposing in 2011 that the blue and red arrows conflate into a single concerted process which does NOT involve an explicit Wheland intermediate ion-pair. The text-books would have to be re-written! Paul Schleyer (a co-author of the above) recently contacted me about this reaction, noting that no explicit intrinsic reaction coordinate (IRC) had been reported in the 2011 article. Could I run one to establish that the course of this reaction really was concerted and “Whelandless“?

The level of theory used before[1] is rb3lyp/6-311++G(2d,2p)/SCRF=CCl4 (the r is added here, for reasons that will soon become apparent) and the animation[2] is shown below, which is followed by repeating the calculation with addition of a D3-type dispersion correction to the core rb3lyp DFT method.[3] Without dispersion, the final HBr becomes H-bonded to the other Br, but with dispersion it instead forms a π-facial hydrogen bond to the aromatic ring. Even for such a small molecule, one can easily observe the effects of dispersion forces!

Br2+benzeneBr2+benzene+D3

br2-d3br2+d3

The reaction is indeed concerted, but it is also asynchronous as revealed by the characteristic feature at IRC ~3. We might conclude that the Wheland does make an appearance in this mechanism, but only as a “hidden intermediate“. It is a relay-race with the blue arrows above running first, and then without pause smoothly passing the baton of the reaction to the red arrows. The activation energy is high, commensurate with a reaction that in fact does not take place at normal temperatures.

Boris Galabov (another co-author[1]) then pointed out to me that the spin-restricted wavefunction (r above) at the transition state is unstable with respect to spin unrestriction.[4] This means that some open-shell biradical character is present at least at the transition state if not the entire pathway. So what would happen if the IRC were repeated using ub3lyp instead of rb3lyp? Would allowing for biradical character still retain the concerted nature?

Before showing the results, I have to point out that the uIRC must be done in two stages, the first being the path to the transition state and the second the path down from it to products (the program I use to show the profiles is not capable has errors when splicing the two together). First the upward path[5] (without dispersion) ending at the TS, followed by the path down.[6]

urE

IRC profile for spin-unrestricted pathway 
ufE
ufG

On the approach path, the spin expectation operator <S2> starts at zero but at IRC ~2.0 it becomes non-zero (biradical character forms) and this persists to the transition state and to IRC ~-2 beyond on the downward path before reverting again to a closed shell singlet. In this central region we have what amounts to a “hidden biradicaloid intermediate”. Since the C-Br bond formation and the subsequent C-H bond cleavage are NOT synchronous, we also retain the hidden Wheland characteristics. So this system is perhaps best described as having a “hidden biradicaloid Wheland intermediate“; a double whammy in the vernacular.  The non zero value of  <S2> lowers the activation barrier from  ~42 kcal/mol to  ~37 kcal/mol, but it still remains a barrier which is insurmountable at room temperatures.

The bottom line remains: according to this quantum model, the reaction is concerted, as originally claimed.[1]


The technical explanation is as follows. The IRC is started at the TS, and the SCF is converged using a broken-symmetry keyword guess(mix). As the IRC proceeds on the path down to reactant, each step uses the density matrix from the previous step as the initial SCF guess. This ensures that the unrestricted wavefunction remains symmetry broken if that is the lowest energy solution. Before the reactant is reached however, <S2> has collapsed to zero. Then the forward path is started, again from the TS. However, the program continues to use the last density matrix and hence <S2> continues to be zero for this entire path. Hence the reason for performing two separate IRC calculations, to ensure that the correct value of <S2> is achieved on both pathways.


References

  1. J. Kong, B. Galabov, G. Koleva, J. Zou, H.F. Schaefer, and P.V.R. Schleyer, "The Inherent Competition between Addition and Substitution Reactions of Br<sub>2</sub> with Benzene and Arenes", Angewandte Chemie International Edition, vol. 50, pp. 6809-6813, 2011. https://doi.org/10.1002/anie.201101852
  2. H.S. Rzepa, "Gaussian Job Archive for C6H6Br2", 2014. https://doi.org/10.6084/m9.figshare.956223
  3. H.S. Rzepa, "Gaussian Job Archive for C6H6Br2", 2014. https://doi.org/10.6084/m9.figshare.956247
  4. M.J. Dewar, S. Olivella, and H.S. Rzepa, "MNDO study of ozone and its decomposition into (O2 + 0)", Chemical Physics Letters, vol. 47, pp. 80-84, 1977. https://doi.org/10.1016/0009-2614(77)85311-6
  5. H.S. Rzepa, "Gaussian Job Archive for C6H6Br2", 2014. https://doi.org/10.6084/m9.figshare.958784
  6. H.S. Rzepa, "Gaussian Job Archive for C6H6Br2", 2014. https://doi.org/10.6084/m9.figshare.958785

Caesium trifluoride: could it be made?

Saturday, November 23rd, 2013

Mercury (IV) tetrafluoride attracted much interest when it was reported in 2007[1] as the first instance of the metal being induced to act as a proper transition element (utilising d-electrons for bonding) rather than a post-transition main group metal (utilising just s-electrons) for which the HgF2 dihalide would be more normal (“Is mercury now a transition element?”[2]). Perhaps this is the modern equivalent of transmutation! Well, now we have new speculation about how to induce the same sort of behaviour for caesium; might it form CsF3 (at high pressures) rather than the CsF we would be more familiar with.[3] Here I report some further calculations inspired by this report.

The argument goes something like this. Xenon difluoride (XeF2) is a well-known stable compound of xenon. Caesium comes immediately after xenon in the periodic table (electron shell properties [Xe].6s1) and so Cs+ would be iso-electronic with Xe. If the latter can form a stable difluoride (and higher), why not Cs? A neutral compound following this line of argument would therefore be CsF3.

So here comes a calculation. I used a large basis set (Def2-QZVPPD basis for Cs), with a pseudopotential describing 46 core electrons (including the two d-shells) and a further 8 in the 5s/p shell to make up the [Xe] core + 1 extra in the 6s shell) using the ωB97XD functional to obtain the geometry, shown below.[4]

Click for 3D

Click for 3D and normal modes

All 3N-6 normal vibrational modes are real, which indicates it is a proper minimum in the potential energy surface. A QTAIM analysis shows that ρ(r) at the bond critical points is pretty respectable for bonds (below). The QTAIM-derived average number of electrons on Cs is 7.4, which gives a charge of 1.6 on the Cs , thus involving the 5p shell as well as the 6s.

CsF3-AIM

The most obvious question is what is the free energy change when the species dissociates to CsF and F2? This is exo-energic by 25.1 kcal/mol[5], not as large as you might have thought! Well, what about the barrier to such dissociation? The transition state for this process is shown below, delightfully asymmetric![6] and this gives a free energy barrier of 33.9 kcal/mol (the IRC smoothly defines this reaction[7],[8]).

Click for animation

Click for animation

We may conclude from this brief foray that in CsF3 caesium would indeed deserve to be called a p-block element, although this is not quite as good as it sounds. Take a look for example at the highest occupied molecular orbital. It certainly involves the p-block, but this orbital is in fact anti-bonding, and the Cs-F bonds derive their strength from the lower occupied orbitals.

Click for  3D

HOMO. Click for 3D

 

Click for 3D

HOMO-6. Click for 3D

And the final take-home message. The report of this molecule[3] suggests it could be stable under high pressure. Here, the free energy barrier to dissociation is calculated to be indeed high, which implies that if made it could be kinetically quite stable even under normal pressures (in an inert matrix where it would be prevented from reacting with itself).

POSTSCRIPT: The LUMO below is also antibonding, but is mostly 6s on Cs. If one force-populates this by a double excitation from the  HOMO, the resulting state is higher in energy (the wavefunction is stable to both singlet and triplet excitations). Which shows that Cs utilises (antibonding) 5p rather than (antibonding) 6s in this species.

CsF3-LUMO

References

  1. X. Wang, L. Andrews, S. Riedel, and M. Kaupp, "Mercury Is a Transition Metal: The First Experimental Evidence for HgF<sub>4</sub>", Angewandte Chemie International Edition, vol. 46, pp. 8371-8375, 2007. https://doi.org/10.1002/anie.200703710
  2. M. Miao, "Caesium in high oxidation states and as a p-block element", Nature Chemistry, vol. 5, pp. 846-852, 2013. https://doi.org/10.1038/nchem.1754
  3. H.S. Rzepa, "Gaussian Job Archive for CsF3", 2013. https://doi.org/10.6084/m9.figshare.861029
  4. H.S. Rzepa, "Gaussian Job Archive for CsF3", 2013. https://doi.org/10.6084/m9.figshare.861030
  5. "Cs 1 F 3", 2013. http://hdl.handle.net/10042/26513
  6. H.S. Rzepa, "Gaussian Job Archive for CsF3", 2013. https://doi.org/10.6084/m9.figshare.861038
  7. H.S. Rzepa, "Gaussian Job Archive for CsF3", 2013. https://doi.org/10.6084/m9.figshare.861047

Caesium trifluoride: could it be made?

Saturday, November 23rd, 2013

Mercury (IV) tetrafluoride attracted much interest when it was reported in 2007[1] as the first instance of the metal being induced to act as a proper transition element (utilising d-electrons for bonding) rather than a post-transition main group metal (utilising just s-electrons) for which the HgF2 dihalide would be more normal (“Is mercury now a transition element?”[2]). Perhaps this is the modern equivalent of transmutation! Well, now we have new speculation about how to induce the same sort of behaviour for caesium; might it form CsF3 (at high pressures) rather than the CsF we would be more familiar with.[3] Here I report some further calculations inspired by this report.

The argument goes something like this. Xenon difluoride (XeF2) is a well-known stable compound of xenon. Caesium comes immediately after xenon in the periodic table (electron shell properties [Xe].6s1) and so Cs+ would be iso-electronic with Xe. If the latter can form a stable difluoride (and higher), why not Cs? A neutral compound following this line of argument would therefore be CsF3.

So here comes a calculation. I used a large basis set (Def2-QZVPPD basis for Cs), with a pseudopotential describing 46 core electrons (including the two d-shells) and a further 8 in the 5s/p shell to make up the [Xe] core + 1 extra in the 6s shell) using the ωB97XD functional to obtain the geometry, shown below.[4]

Click for 3D

Click for 3D and normal modes

All 3N-6 normal vibrational modes are real, which indicates it is a proper minimum in the potential energy surface. A QTAIM analysis shows that ρ(r) at the bond critical points is pretty respectable for bonds (below). The QTAIM-derived average number of electrons on Cs is 7.4, which gives a charge of 1.6 on the Cs , thus involving the 5p shell as well as the 6s.

CsF3-AIM

The most obvious question is what is the free energy change when the species dissociates to CsF and F2? This is exo-energic by 25.1 kcal/mol[5], not as large as you might have thought! Well, what about the barrier to such dissociation? The transition state for this process is shown below, delightfully asymmetric![6] and this gives a free energy barrier of 33.9 kcal/mol (the IRC smoothly defines this reaction[7],[8]).

Click for animation

Click for animation

We may conclude from this brief foray that in CsF3 caesium would indeed deserve to be called a p-block element, although this is not quite as good as it sounds. Take a look for example at the highest occupied molecular orbital. It certainly involves the p-block, but this orbital is in fact anti-bonding, and the Cs-F bonds derive their strength from the lower occupied orbitals.

Click for  3D

HOMO. Click for 3D

 

Click for 3D

HOMO-6. Click for 3D

And the final take-home message. The report of this molecule[3] suggests it could be stable under high pressure. Here, the free energy barrier to dissociation is calculated to be indeed high, which implies that if made it could be kinetically quite stable even under normal pressures (in an inert matrix where it would be prevented from reacting with itself).

POSTSCRIPT: The LUMO below is also antibonding, but is mostly 6s on Cs. If one force-populates this by a double excitation from the  HOMO, the resulting state is higher in energy (the wavefunction is stable to both singlet and triplet excitations). Which shows that Cs utilises (antibonding) 5p rather than (antibonding) 6s in this species.

CsF3-LUMO

References

  1. X. Wang, L. Andrews, S. Riedel, and M. Kaupp, "Mercury Is a Transition Metal: The First Experimental Evidence for HgF<sub>4</sub>", Angewandte Chemie International Edition, vol. 46, pp. 8371-8375, 2007. https://doi.org/10.1002/anie.200703710
  2. M. Miao, "Caesium in high oxidation states and as a p-block element", Nature Chemistry, vol. 5, pp. 846-852, 2013. https://doi.org/10.1038/nchem.1754
  3. H.S. Rzepa, "Gaussian Job Archive for CsF3", 2013. https://doi.org/10.6084/m9.figshare.861029
  4. H.S. Rzepa, "Gaussian Job Archive for CsF3", 2013. https://doi.org/10.6084/m9.figshare.861030
  5. "Cs 1 F 3", 2013. http://hdl.handle.net/10042/26513
  6. H.S. Rzepa, "Gaussian Job Archive for CsF3", 2013. https://doi.org/10.6084/m9.figshare.861038
  7. H.S. Rzepa, "Gaussian Job Archive for CsF3", 2013. https://doi.org/10.6084/m9.figshare.861047

Multiple personalities of Magnesium.

Tuesday, November 5th, 2013

The following is a short question in a problem sheet associated with introductory organic chemistry.

  • Q: “Show curly arrows for the formation of the product of the following reaction, together with a Lewis representation of that product: Et2O + MgBr2“.
  • AEt2O+-MgBr2 (a product by the way that is known as magnesium bromide ethyl etherate, and which is commercially available as a solution).

First a few tutor-like comments. The Mg is tri-coordinate in this simple representation, and if we assume that the bonds are covalent, has six electrons in the Mg valence shell. In modern notation, the Mg has a formal charge of -1 and the oxygen +1. The Mg thus does not have a filled 3s/3p valence shell, which would be eight. But few (students or tutors) go on to apply a reality check. So here is one.

The reality check involves a search for a crystal structure, which is really trivial to set up. And what we find are the following.

  1. The first hit with exactly this stoichiometry has the CCDC code TOQKIT and a polymeric structure as below. Each Mg is coordinated by four (bridged) bromines and one oxygen, giving trigonal bipyramidal penta-coordination. The valence electron count at Mg is now eight, but distributed around five bonds, not four. Since we no longer have formal Lewis two-electron covalent bonds, it is difficult to assign a Lewis-like charge to the atoms. 
    Click for  3D

    Click for 3D

  2. The next hit actually corresponds to the stoichiometry 2R2O + MgBr2 (R=thf). This again is polymeric, but differs from the first structure in having octahedral Mg (six coordination).
    Click for  3D.

    Click for 3D.

  3. OK, even more ether: 4R2O + MgBr2. Finally, non polymeric but again with six-coordinate octahedral Mg. The Mg again has a filled valence octet, and again the bonds are not two-electron ones, hence no charges are attempted. So just a change in the stoichiometry can result in fascinating changes to the resulting structure.
    Click for  3D

    Click for 3D

  4. Finally, a variation; benzyl magnesium bromide (a Grignard reagent) shows tetrahedral coordination.
Click for 3D

Click for 3D

Students (and tutors) who get as far as this are amply rewarded I hope!

Is CLi6 hypervalent?

Friday, July 5th, 2013

A comment made on the previous post on the topic of hexa-coordinate carbon cited an article entitled “Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry[1] by Kudo as a amongst the earliest of evidence that such species can exist (in the gas phase). It was a spectacular vindication of the earlier theoretical prediction[2],[3] that such 6-coordinate species are stable with respect to dissociation to CLi4 and Li2.

The terminology describes these lithium carbides as effectively hypervalent; Kudo in the abstract of his 1992 article uses the more explicit phrase “carbon can expand its octet of electrons to form this relatively stable molecule“. We are taught early on in chemistry that the carbon octet is due to double occupation of four molecular orbitals formed using linear combinations derived from the relatively low energy 2s/2p carbon atomic orbital basis. Octet expansion on carbon must therefore involve to some degree the next atomic shell (3s/3p), which is normally regarded as too high in energy to be capable of significant population for carbon. But use of the 3s/3p shell seems at first sight inevitable. If one constructs an octahedral complex CLi6 surely ten electrons must be involved in bonding, four from the carbon and six from the equivalent lithiums? The 3s/3p carbon population must therefore be ~2 electrons, and we can truly describe a molecule where carbon has of necessity expanded its octet of electrons to ten as hypervalent. Or can we?

How does a quantitative (ωB97XD/6-311++G(d) ) calculation[4] reveal this effective hypervalency? 

  1. The octahedral geometry is indeed a stable minimum, with the lowest vibrational wavenumber being 194 cm-1.
  2. It also checks out as clearly a closed shell species, stable to open shell perturbations.
  3. An NBO analysis reveals the Rydberg population (those 3s/3p atomic orbitals) to be only 0.09 electrons.
  4. It partitions the electrons into 13.97 for the 1s cores of the seven atoms, 7.67 “valence-Lewis” (i.e. shared covalent) and a mysterious 2.27 (valence, non-Lewis).

We now have a problem. One of the standard methods for partitioning electrons has isolated two of our ten electrons and placed them, with small partial occupancy, into unshared “lone pairs”, located as it happens on the lithium atoms (shown below for one of these partial lone “pairs”). The carbon is NOT hypervalent, and it has NOT expanded its octet.

Click for  3D

Click for 3D

So I tried another procedure, deliberately chosen to be rather different from the orbital-based NBO formalism. This is analysis of the ELF, or electron localisation function, and represents an attempt to derive the result based on a function related to the electron density. The red spheres shown below are the centroids of the twelve ELF basins located:

Click for  3D

Click for 3D

Each of these (equivalent) basins has an electron population of ~0.81, making ~9.7 electrons in total. Each lithium sits on a square arrangement of four of these basins, and so has access to ~3.2 valence electrons. How do we interpret the situation for carbon however? Does its valence shell contain an expanded 9.7 electrons? Well, not necessarily. You can see that each of the basins has a three-centre relationship between the one carbon and TWO lithiums. These electrons contribute not just to C-Li bonding, but also to Li…Li bonding. So these 9.7 electrons contribute in part to bonding that does NOT involve the carbon. We can see this in the (Wiberg) bond orders, 0.254 for the C-Li interaction, and 0.116 for adjacent Li…Li interactions (such an explanation was also suggested for why II7 has no expanded octet at the central iodine). In fact, the origins of this effect were first clearly identified in the theoretical analysis of 1983[3]: “the extra electrons beyond the usual octet are involved with metal-metal bonding rather than with interactions of the metals with the central atoms“.

It is nice to see that despite the passage of 30 years, and despite the introduction of many new ways of analysing the wavefunctions and hence the bonding of molecules, the essential original interpretation[3] remains robustly correct! 

References

  1. H. Kudo, "Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry", Nature, vol. 355, pp. 432-434, 1992. https://doi.org/10.1038/355432a0
  2. E.D. Jemmis, J. Chandrasekhar, E.U. Wuerthwein, P.V.R. Schleyer, J.W. Chinn, F.J. Landro, R.J. Lagow, B. Luke, and J.A. Pople, "Lithiated carbocations. The generation, structure, and stability of CLi5+", Journal of the American Chemical Society, vol. 104, pp. 4275-4276, 1982. https://doi.org/10.1021/ja00379a051
  3. P.V.R. Schleyer, E.U. Wuerthwein, E. Kaufmann, T. Clark, and J.A. Pople, "Effectively hypervalent molecules. 2. Lithium carbide (CLi5), lithium carbide (CLi6), and the related effectively hypervalent first row molecules, CLi5-nHn and CLi6-nHn", Journal of the American Chemical Society, vol. 105, pp. 5930-5932, 1983. https://doi.org/10.1021/ja00356a045
  4. "C 1 Li 6", 2013. http://hdl.handle.net/10042/24790

Streptomycin: a case study in the progress of science.

Monday, May 28th, 2012

Streptomycin is an antibiotic active against tuberculosis, and its discovery has become something of a cause célèbre. It was first isolated on October 19, 1943 by a graduate student Albert Schatz in the laboratory of Selman Waksman at Rutgers University. I want to concentrate in this post on its molecular structure. Its initial isolation was followed by an extraordinarily concentrated period of about three years devoted to identifying that structure, culminating in a review of this chemistry in 1948 by Lemieux and Wolfram.[1] This review presents the structure as shown below (left). The modern rendering on the right is based on a crystal structure done in 1978.[2]

My interest in this was kindled by wondering how elucidating such a structure would be accomplished during the 1940s. None of the modern structural techniques were available then (NMR, MS, X-Ray); only IR and polarimetry (optical rotation). So how was it done? Well, the same way it had been done for the previous 100 years or so; degradation. In this case, into three smaller fragments, labelled A-C in the rhs diagram, and named streptidine, streptose and glucosamine in the original analysis.

  1. This reduction to smaller fragments is set out on page 338 of the Lemieux and Wolfram article.[1]
  2. The procedure to isolate streptomycin is described from p343 and the purification on p345, which concludes with the molecular formula C21H37-39N7O12
  3. On p346, after evaluating other methods for determining the molecular weight, C21H39N7O12 is the final candidate for its formula.
  4. Next, “strongly basic” degradation yields streptidine (Ring C), with the formula C8H18N6O4. Likewise, formulae were established for the other components.
  5. On p347, the odyssey to assemble a structure from this information begins. I will not dwell on the details. But by p359, a partial structure of Streptidine-streptose-N-methyl-L-glucosamine is suggested.
  6. By p366, they have boiled it down to two possibilities (they call XXXIX and XL), and they abandon the hydrolytic procedures used up to that point and adopt oxidative reactions, which narrow it down to XXXIX.
  7. The next property to be used to determine the structure is optical rotation. They knew it incorporates an L-sugar (whose absolute configuration was not known in 1948), and of course there are 15 stereogenic centres in the entire system (32768 possibilities). P368 -375 continues discussion of the stereochemistry, and in particular the need to demonstrate that none of the degradative/oxidative procedures have interfered with it, so to speak.
  8. By p375, it has all boiled down to the stereochemistry of the glycosidic bonds (marked with a red ring above). This was assigned on the basis of optical rotations and the use of additive rules (Table 1 of their article). This discussion ends with the stereochemistry shown above. Although initially assigned trans, it was subsequently revised to cis, and then back to trans again.
  9. On p382, the wrap up has started. Table III there shows the properties of the 18 products obtained merely from the preparation of ring A (for comparison with the product obtained by degradation). Some 127 articles have been cited for supporting information and around 50 pages of tight logical argument presented as evidence, similar in length indeed to the longer mathematical proofs!
  10. There was one residual uncertainty (green ring above) that had to wait for the crystal structure in 1978 to resolve. It took so long because of the challenge of finding a crystalline derivative.

I cannot help but note that the skills required to assemble a structure by degradation, and no use of NMR, MS or X-ray, were formidable, and very probably there are few chemists alive nowadays who could do a similar job (the motivation to do so would also be lacking). Assuming good crystals were available, solving such a structure nowadays using crystallography would only take 24 hours or so. And structures with 100+ stereogenic centres can now be done. When Woodward mused about the progress in chemistry, he might have had streptomycin in mind. I think it is worth remembering that the structural chemistry of 60 years ago was quite an intellectual achievement.

References

  1. R. Lemieux, and M. Wolfrom, "The Chemistry of Streptomycin", Advances in Carbohydrate Chemistry, pp. 337-384, 1948. https://doi.org/10.1016/s0096-5332(08)60034-x
  2. S. Neidle, D. Rogers, and M.B. Hursthouse, "The crystal and molecular structure of streptomycin oxime selenate tetrahydrate", Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences, vol. 359, pp. 365-388, 1978. https://doi.org/10.1098/rspa.1978.0047

Nobelocene: a (hypothetical) 32-electron shell molecule?

Friday, April 29th, 2011

The two previous posts have explored one of the oldest bonding rules (pre-dating quantum mechanics), which postulated that filled valence shells in atoms forming molecules follow the magic numbers 2, 8, 18 and 32. Of the 59,025,533 molecules documented at the instant I write this post, only one example is claimed for the 32-electron class. Here I suggest another, Nobelocene (one which given the radioactive instability of nobelium, is unlikely to be ever confirmed experimentally!)

Nobelium has the electronic configuration [Rn].5f14.7s2 , which means the 6d and 7p shells are still empty. Filling these would take 10+6 electrons, or four more electrons (20) if one starts from No4+, resulting in a complete 32-electron filled shell for the Nobelium. These twenty electrons could be provided by two cyclo-octatetraenyl (COT) dianion ligands. Nobelium, with its nuclear charge of +102, has highly relativistic inner-shell electrons, and so special techniques must be used to model this. Here I have used a SARC all electron relativistically contracted basis set (DOI: 10.1021/ct100736b), to be used with the Douglas−Kroll−Hess scalar relativistic Hamiltonian (for details, see here). The QTAIM analysis is shown below (quite a spider’s web):

Nobelocene. AIM analysis. Click for 3D.

There are 16 bond critical points located along the lines of each No..C, with ρ(r) 0.03. This is a very low value indeed for a covalent bond, being of the same order as strong hydrogen bonds, and so should be classed as an interaction rather than a bond. ELF basins cannot normally be located for hydrogen bonds, and neither can they here. Nobelocene in this regard is pretty boring, being almost entirely ionic.

ELF analysis for Nobelocene.

Rather more interesting are the molecular orbitals. The most stable π-type is shown below. Many of the orbitals show the Nobelium atomic orbitals non-interacting with the ligand, probably because the relativistic contraction renders them inert to mixing, in a manner which is often used to explain the inert nature of e.g. the Pb 6s2 electrons in divalent lead.

Molecular orbital for nobelocene. Click for 3D.

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

Ferrocene

Sunday, April 17th, 2011

The structure of ferrocene was famously analysed by Woodward and Wilkinson in 1952 (DOI: 10.1021/ja01128a527), symmetrically straddled in history by Pauling (1951) and Watson and Crick (1953). Quite a trio of Nobel-prize winning molecular structural analyses, all based on a large dose of intuition. The structures of both proteins and DNA succumbed to models built from simple Lewis-type molecules with covalent (and hydrogen) bonds; ferrocene is intriguingly similar and yet different. Similar because Lewis postulated an octet of electrons as being key to the (quadri)valencies of e.g. carbon via four electron pair bonds. He did not (in 1916) realise that 8 = 2(1 + 3), and that the next in sequence would be 18 = 2(1 + 3 + 5). That would have to wait for quantum mechanics, and of course inorganic chemists now call it the 18-electron rule (for an example of the 32-electron rule, or 2+6+10+14, as first suggested by Langmuir in 1921[1] (see also here).

Iron has an argon core, and 6 (of a maximum of 10) 3d electrons, 2 (of a maximum of 2) 4s, and 0 (of a maximum of 6) 4p electrons. Or, 8 = 2 + 0 + 6 rather than 18 = 2 + 6 + 10. So Woodward and Wilkinson argued that sharing a further 10 electrons would bring iron up to, in effect, a Lewis shell (albeit one using not just s and p shells, but d shells too). These 10 electrons would be provided by two cyclopentadienyl radicals. Thence a Nobel prize (for Wilkinson)! But wait!

QTAIM analysis for Ferrocene. Green=bcp, red=rrp, blue=ccp.

Firstly, let me adjust slightly the counting above. Rather than starting with neutral Fe, we ionise it to Fe2+. Rather than starting with two cyclopentadienyl radicals, let us use two aromatic cyclopentadienyl anions. But now, Lewis’ idea of covalency via shared electron pair bonds struggles. If 18 electrons really are being deployed (12 from the cyclopentadienyl anions, 6 from the Fe2+), does that imply 9 shared electron-pair bonds? How might the bonds in ferrocene be represented? This matters. Since the 1970s, the idea of searching for molecules via what is called its connectivity (a simple index which ignores bond order, and simply specifies whether two atoms are connected by a bond, any kind of bond, or not) has revolutionised searching for molecules. Think of CAS, Pubchem, REAXYS, CCDC, and SMILES and InChI. So is it useful to try to partition 9 bonds into ferrocene (it kind of difficult, since it has five-fold symmetry)? Indeed, most students trying to search for a ferrocene in any of the aforementioned databases will scratch their head over this one. The normal solution is to draw 10 bonds from the iron, one to each of the ten carbon atoms (and the databases accept this as a valid search query). But what can that mean?

To find out, I show here a QTAIM and an ELF analysis of the bonds (in italics, since we do not know if these conform to Lewis covalent bonds or not). The QTAIM is shown above, and it shows a bond-critical point along all ten of the Fe…C regions. The electron density, ρ(r) at each of these is 0.083 au. In truth, this is rather low, even for a single bond. The Laplacian ∇2ρ(r) at each of these points is +0.29, which is in what Hiberty and Shaik have called the charge-shift category (i.e. NOT a covalent bond). The Laplacian isosurface is shown below, contoured at 0.25, and you can see each of the bond-critical points for the ten Fe-C regions is shrouded in blue (a positive Laplacian). So, NOT a pure covalent two-electron bond of the Lewis variety then(?).

Electronic Laplacian for ferrocene. Click for 3D

How about how many electrons are there in these Fe-C bonds? Enter that other method known as ELF (also the subject of many blog posts here, go searching if you want to find out more).;

 

Centroids of ELF basins for ferrocene. Click for 3D.

Yes, there again are C-Fe disynaptic basins! But the integration of the basin is a measly 0.3e (of ~3.1 electrons for all ten Fe-C bonds). Of course, ELF can detect the difference between covalency and ionicity (the disynaptic basins vanish for ionic bonds), and the low basin count suggests a fair degree of the latter. The ELF function itself is pretty, and is shown below.

 

ELF isosurface for ferrocene. Click for 3D

We can see that ferrocene has departed a long way from Lewis’ model of an electron pair bond, or perhaps even from the covalent bond. But at least we can be assured that the connection table often used for searching for ferrocene and its derivatives is not a fiction! Next, uranocene!

 

References

  1. I. Langmuir, "Types of Valence", Science, vol. 54, pp. 59-67, 1921. https://doi.org/10.1126/science.54.1386.59

Shorter is higher: the strange case of diberyllium.

Friday, January 21st, 2011

Much of chemistry is about bonds, but sometimes it can also be about anti-bonds. It is also true that the simplest of molecules can have quite subtle properties. Thus most undergraduate courses in chemistry deal with how to describe the bonding in the diatomics of the first row of the periodic table. Often, only the series C2 to F2 is covered, so as to take into account the paramagnetism of dioxygen, and the triple bonded nature of dinitrogen (but never mentioning the strongest bond in the universe!). Rarely is diberyllium mentioned,  and yet by its strangeness, it can also teach us a lot of chemistry.

The diagram below is what many textbooks show. The diagram can vary (and hence confuse) slightly, in regard to the relative ordering of the σ and π energy levels originating from the overlap of the 2p orbitals. It depends on the atom, and for Be, the σ comes out higher than the π. The other key ordering is that the σ* antibonding orbital resulting from out of phase overlap of the two 2s orbitals is actually lower in energy than the π bonding orbital resulting from in-phase overlap of the 2p orbitals. Yes, an antibonding orbital is more stable than a bonding orbital!

Molecular orbital diagram for Be2

Well, the diagram shows that the pair of occupied molecular orbitals resulting from the two (symmetric and antisymmetric, or g and u) combinations of the 1s orbitals cancel each other, as do the 2s combinations, and we conclude the bond order for this molecule is zero! Actually, if a quantum mechanical calculation is performed (at the ωB97XD/6-311G(d,p) level), the bond length emerges as 2.81Å and a vibrational wavenumber of 167 cm-1 is predicted. Despite the zero bond order, a weak bond IS predicted, and this is the van der Waals or dispersion bond.

Let us now pump this molecule up to a higher energy state by a double excitation of the two electrons in the 2s σ* electrons. We have to split them up, one each, into the next available orbital, which is the π, to form a triplet state (just like di-oxygen).

The doubly excited state of diberyllium

Well, this (higher energy) state is certainly shorter (a contrast with my item on longer being stronger). The length is now 1.78Å, which is more than 1Å shorter than the original state, despite being ~ 45 kcal/mol higher in energy. The Be-Be stretching wavenumber goes up to 917 cm-1. With four electrons in bonding orbitals, diberyllium has a double bond! One can also pair the π electrons up to form an open shell (excited) singlet, which is ~ 51 kcal/mol higher than the closed shell (unbonded) singlet. This also has a length of 1.78Å and a marginally lower stretch of 909 cm-1. If you want to read more about the doubly excited state of this molecule, see DOI: 10.1139/v96-111.

One might be tempted to make an analogy between physics, and its particles and antiparticles. Yes, electrons can occupy antibonding as well as bonding orbitals. But the overall bond order will be reduced to zero if the total numbers of each are equal. And one can be pretty certain that there is no molecule at all in which the number of antibonding electrons exceeds the bonding ones! Or, if anyone is aware of such an example, do tell!