Posts Tagged ‘Reducing agents’

Hypervalent Helium – not!

Friday, February 16th, 2018

Last year, this article[1] attracted a lot of attention as the first example of molecular helium in the form of Na2He. In fact, the helium in this species has a calculated‡ bond index of only 0.15 and it is better classified as a sodium electride with the ionisation induced by pressure and the presence of helium atoms. The helium is neither valent, nor indeed hypervalent (the meanings are in fact equivalent for this element). In a separate blog posted in 2013, I noted a cobalt carbonyl complex containing a hexacoordinate hydrogen in the form of hydride, H–. A comment appended to this blog insightfully asked about the isoelectronic complex containing He instead of H–. Here, rather belatedly, I respond to this comment!

The complex [HCo6(CO)15]– has a calculated bond index at the hydrogen of 0.988 and a calculated NMR chemical shift of 21.6 ppm (ωB97XD/Def2-TZVPPD calculation) compared to a measured value of 23.2 ppm. Despite being six-coordinate, the hydride has a bond index that does not exceed one (it is not hypervalent).

So here is the neutral helium analogue. The He bond index emerges as 0.71 at the geometry of the hydride complex. Compare this with the bond index of 0.15 calculated for Na2He and it would be fair to say that at this geometry, the helium in [HeCo6(CO)15] would have a greater claim to be a molecular compound. Back in 2010, extrapolating from a series of posts here, I had speculated[2] about other molecular species of He, including the di-cation below. This has a He bond index of 0.54, rather less than that in [HeCo6(CO)15] but much more than in Na2He. It is also vibrationally stable.

But now, [HeCo6(CO)15] goes “pear-shaped” (why do pears have such a bad press?). I started a process of optimizing the geometry of this complex (ωB97Xd/Def2-TZVPPD). Slowly, the He started to creep out of the centre of the complex and emerge from the cavity. After about 100 steps it reached the geometry shown below, at which point the Wiberg bond index has dropped to 0.62 and still going down. I think it might take a few more steps to be completely expelled, but I have stopped the geometry optimisation at this stage.

So helium appears not to be valent in [HeCo6(CO)15]. However, I have yet to try Ne, which is both larger and softer. I will post results here.

‡All data at 10.14469/hpc/3587.

References

  1. X. Dong, A.R. Oganov, A.F. Goncharov, E. Stavrou, S. Lobanov, G. Saleh, G. Qian, Q. Zhu, C. Gatti, V.L. Deringer, R. Dronskowski, X. Zhou, V.B. Prakapenka, Z. Konôpková, I.A. Popov, A.I. Boldyrev, and H. Wang, "A stable compound of helium and sodium at high pressure", Nature Chemistry, vol. 9, pp. 440-445, 2017. https://doi.org/10.1038/nchem.2716
  2. H.S. Rzepa, "The rational design of helium bonds", Nature Chemistry, vol. 2, pp. 390-393, 2010. https://doi.org/10.1038/nchem.596

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Posted in Hypervalency | 4 Comments »

Pyrophoric metals + the mechanism of thermal decomposition of magnesium oxalate.

Sunday, March 19th, 2017

A pyrophoric metal is one that burns spontaneously in oxygen; I came across this phenomenon as a teenager doing experiments at home. Pyrophoric iron for example is prepared by heating anhydrous iron (II) oxalate in a sealed test tube (i.e. to 600° or higher). When the tube is broken open and the contents released, a shower of sparks forms. Not all metals do this; early group metals such as calcium undergo a different reaction releasing carbon monoxide and forming calcium carbonate and not the metal itself. Here as a prelude to the pyrophoric reaction proper, I take a look at this alternative mechanism using calculations.


There are ~60 crystal structures of metal oxalates, of which several are naturally occurring minerals (Fe, humboldtine[1], Ca, Weddellite[2], Li[3], Na[4], K[5], Cs[6]. The natural geometry of the oxalate di-anion is planar (torsion 0 or 180°) but a small number are twisted such as the caesium oxalate.

The kinetics of pyrolysis of a number of metal  oxalates were studied some years ago (Ca[7], Li[8]) indicating barriers ranging from 53-68 kcal/mol. One proposed mechanism is as shown in this article.[7]

It was surmised from the kinetic analysis that the k1 activation step (rotation about the C-C bond from planar to twisted) was ~12 ± 20 kcal/mol, whilst steps k2 or k3 had the much higher activation energy noted above. A search (of Scifinder) for quantum mechanical “reality checks” of this mechanism revealed a blank and so I apply such a check here using Mg as the metal.

The carbonyl extrusion step (ωB97XD/Def2-TZVPPD/SCRF=water, DOI: 10.14469/hpc/2320) was studied with a water solvent field applied in an effort to mimic the solid state crystal structure of the species as a better representation of the ionic lattice than a pure vacuum calculation.An IRC (intrinsic reaction coordinate, DOI: 10.14469/hpc/2324) reveals the start-point geometry still has a very small negative force constant (-38 cm-1, DOI: 10.14469/hpc/2321) which now corresponds to a small rotation about the C-C bond to give a C2-symmetric conformation:

But the barrier for this process is tiny and nothing like the ~12 ± 20 kcal/mol inferred from the kinetic analysis. Perhaps most of the incentive to pack into a totally planar geometry comes from the interactions in the ionic lattice. The calculated free energy barrier (ΔG298‡ 54.7 kcal/mol, ΔG755‡ 55.1 kcal/mol) is within the reported measured range.

The mechanism for production of pyrophoric metal itself is likely to be far more complex, involving (inter alia) electron transfer from oxygen to metal. If I find anything I will report back here.

References

  1. T. Echigo, and M. Kimata, "Single-crystal X-ray diffraction and spectroscopic studies on humboldtine and lindbergite: weak Jahn–Teller effect of Fe2+ ion", Physics and Chemistry of Minerals, vol. 35, pp. 467-475, 2008. https://doi.org/10.1007/s00269-008-0241-7
  2. C. Sterling, "Crystal structure analysis of weddellite, CaC2O4.(2+x)H2O", Acta Crystallographica, vol. 18, pp. 917-921, 1965. https://doi.org/10.1107/s0365110x65002219
  3. https://doi.org/
  4. G.A. Jeffrey, and G.S. Parry, "The Crystal Structure of Sodium Oxalate", Journal of the American Chemical Society, vol. 76, pp. 5283-5286, 1954. https://doi.org/10.1021/ja01650a007
  5. Dinnebier, R.E.., Vensky, S.., Panthofer, M.., and Jansen, M.., "CCDC 192180: Experimental Crystal Structure Determination", 2003. https://doi.org/10.5517/cc6fzcy
  6. Dinnebier, R.E.., Vensky, S.., Panthofer, M.., and Jansen, M.., "CCDC 192182: Experimental Crystal Structure Determination", 2003. https://doi.org/10.5517/cc6fzf0
  7. F.E. Freeberg, K.O. Hartman, I.C. Hisatsune, and J.M. Schempf, "Kinetics of calcium oxalate pyrolysis", The Journal of Physical Chemistry, vol. 71, pp. 397-402, 1967. https://doi.org/10.1021/j100861a029
  8. D. Dollimore, and D. Tinsley, "The thermal decomposition of oxalates. Part XII. The thermal decomposition of lithium oxalate", Journal of the Chemical Society A: Inorganic, Physical, Theoretical, pp. 3043, 1971. https://doi.org/10.1039/j19710003043

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Posted in crystal_structure_mining, reaction mechanism | 1 Comment »

Azane oxide, a tautomer of hydroxylamine.

Friday, April 15th, 2016

In the previous post I described how hydronium hydroxide or H3O+…HO–, an intermolecular tautomer of water, has recently been observed captured inside an organic cage[1] and how the free-standing species in water can be captured computationally with the help of solvating water bridges. Here I explore azane oxide or H3N+-O–,‡ a tautomer of the better known hydroxylamine (H2N-OH).

The usual search[2] of the Cambridge structure database reveals only two (related) entries[3],[4] the second reported in 2015.[5].

NH3-8
NH3-8

Now, location of hydrogen atoms is always a bit tricky, but here we see two species H3N+-OH…–O-+NH3 connected by a strong hydrogen bond of 1.54Å (click on the above image to see this packing). However, it is noteworthy that the N-O bonds for each of these species are exactly the same length (1.412Å); one might have imagined that whether the oxygen carries a proton or not would affect its bond length to nitrogen. There is here a strong hint that energetically the azane oxide might be relatively low in energy relative to hydroxylamine and perhaps that the zwitterionic form might be favoured when captured with hydrogen bonds.

So certainly time for a computational exploration of this species. I am using the three water bridges as before, each comprised of three water molecules and the ωB97XD/6-311++G(d,p)/SCRF=water method. In fact the structure optimises[6] to a delightful propeller-like geometry in which bridges are formed from both two AND three waters across the ion-pair, with overall three-fold C3 symmetry (i.e. chiral! Indeed, this species has a predicted optical rotation of 40° at 589nm).

NH3-8

Hydroxylamine itself has a less symmetric arrangement of hydrogen bonds[7], with a free energy in fact very similar (within 1 kcal/mol) to the ion-pair isomer. Here, a stochastic (statistical) exploration of all the various arrangements of water would be needed to be confident that the lowest energy form had been located. I would note that the N-O bond lengths in the ion-pair and neutral forms are respectively 1.399 and 1.435Å.

NH3-8

Certainly, this very brief computational look at azane oxide suggests that concentrations of this species in aqueous solutions of hydroxylamine might be appreciable (detectable). Its "trapping" inside a suitably designed cavity must be a realistic possibility (the cavity used to trap hydronium hydroxide probably does not have the correct dimensions for this purpose), as indeed illustrated in the two crystal structures noted above.

‡ I have represented this species in ionic form, but you may find text books showing it in dative form, or H3N→O. My personal inclination is to always prefer the ionic form, if only because it enables connections/analogies such as the one here to hydronium hydroxide to be more easily made.

References

  1. M. Stapf, W. Seichter, and M. Mazik, "Unique Hydrogen‐Bonded Complex of Hydronium and Hydroxide Ions", Chemistry – A European Journal, vol. 21, pp. 6350-6354, 2015. https://doi.org/10.1002/chem.201406383
  2. H. Rzepa, "Search for Azane oxide", 2016. https://doi.org/10.14469/hpc/380
  3. Fischer, Dennis., Klapotke, Thomas M.., and Stierstorfer, Jorg., "CCDC 1054611: Experimental Crystal Structure Determination", 2015. https://doi.org/10.5517/cc14ddqn
  4. Fischer, D.., Klapotke, T.M.., and Stierstorfer, J.., "CCDC 827687: Experimental Crystal Structure Determination", 2012. https://doi.org/10.5517/ccws8lh
  5. D. Fischer, T.M. Klapötke, and J. Stierstorfer, "1,5‐Di(nitramino)tetrazole: High Sensitivity and Superior Explosive Performance", Angewandte Chemie International Edition, vol. 54, pp. 10299-10302, 2015. https://doi.org/10.1002/anie.201502919
  6. H.S. Rzepa, "H 21 N 1 O 10", 2016. https://doi.org/10.14469/ch/192000
  7. H.S. Rzepa, "H 21 N 1 O 10", 2016. https://doi.org/10.14469/ch/192001

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Posted in General, Interesting chemistry | No Comments »