Posts Tagged ‘energy relative’

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

Tags:, , , , , , , , , , , , , ,
Posted in General, Interesting chemistry | No Comments »

Yes, no, yes. Computational mechanistic exploration of (nickel-catalysed) cyclopropanation using tetramethylammonium triflate.

Thursday, October 1st, 2015

A fascinating re-examination has appeared[1] of a reaction first published[2] in 1960 by Wittig and then[3] repudiated by him in 1964 since it could not be replicated by a later student. According to the new work, the secret to a successful replication seems to be the presence of traces of a nickel catalyst (originally coming from e.g. a nickel spatula?). In this recent article[1] a mechanism for the catalytic cycle is proposed. Here I thought I might explore this mechanism using calculations to see if any further insights might emerge.

cyclopropanation

In the mechanism above (I have retained the original numbering shown in the article itself), Ln is set to 2PH3 as an initial approximation and the solvent thf is approximated only by a continuum solvation field, with no explicit thf molecules involved at this stage. At this level and using ωB97XD/Def2-SVPD/SCRF=thf free energies, one can explore the cycle quite quickly (~2-3 days). It is also interesting that this reaction unusually involved nine different elements (I wonder what the record is? Not much greater I suspect).

Species ΔΔG298 DataDOI
4+CH2NMe3+LiOTf + ethene +23.9 [4],[5]
5 0.0 [6]
TS (5→ 9) 12.7 [7],[8]
9 + LiOTf + NMe3 0.2 [9]
TS (9 + ethene → 6) 7.2 [10],[11]
6 4.8 [12]
TS (6 → 7) 11.2 [13],[14]
7 -36.3 [15]
TS (7 → 4+8) -18.8 [16],[17]
4+8 + LiOTf + NMe3 -29.7 [4]

The structure of the complex 5 is more or less as shown in the article. The mean single bonded Ni-C length in the Cambridge structure database (CSD) is ~1.9Å, and (formally at least) Ni=C lengths are shorter at ~1.80-1.85. There is one reasonable analogy to the sub-structure shown below[18],[19] with a C-Ni length of 1.90, Ni-Li = 2.51 and Li-C = 2.40 which is reasonably similar to what is shown below. 

T

Click for 3D

Click for 3D

The elimination of NMe3 reveals a reasonable thermal barrier, resulting in the formation of the nickel-carbene product and the complex between NMe3 and LiOTf. 

5a5-9

The Ni-carbene then reacts with alkene (modelled here by ethene) to form a Ni-alkene π-complex, with a very low barrier to the exo-energic reaction.

9-6a9-6

This complex then rearranges, again with a small barrier, to the metallocyclobutane, with considerable release of energy.

6-7a6-7

Finally, the metallocyclobutane extrudes the nickel to form cyclopropane bound to the Ni(PH3)2 as a pseudo-π/agostic complex, with this step of the reaction being somewhat endo-energic (+6.6 kcal/mol). As modelled, it produces a low-coordination Ni product 4, which also causes the initial reactants to be relatively high in energy (+23.9 relative to 5). This suggests that the entire cycle should optimally be repeated by including say two explicit thf solvent molecules, which could coordinate to 4, thus lowering its energy relative to the rest of the cycle. 

7-4a7-4

Below is shown the NCI (non-covalent-interactions) surface for the Ni-cyclopropane complex, revealing the relatively high density between the Ni and the edge of the cyclopropane (high enough indeed to be considered on the verge of being covalent density). No examples of this motif are found in the CSD.

Click for 3D

Click for 3D


Overall, the reaction as shown shows entirely reasonable energetics and activation free energy barriers (with the caveat that inclusion of explicit solvent molecules might improve things, see above). We might conclude from this that the catalytic cycle as proposed is entirely reasonable. What we cannot comment on of course is the relative energetics of any of the competing side reaction shown in the original scheme,[1] but it would be really easy to include them in a more complete analysis if needed. I wanted to show here that a simple reality check on a proposed reaction mechanism can be quick to perform, and perhaps nowadays should be regarded as a sine qua non of mechanistic speculation.

References

  1. S.A. Künzi, J.M. Sarria Toro, T. den Hartog, and P. Chen, "Nickel‐Catalyzed Cyclopropanation with NMe<sub>4</sub>OTf and <i>n</i>BuLi", Angewandte Chemie International Edition, vol. 54, pp. 10670-10674, 2015. https://doi.org/10.1002/anie.201505482
  2. V. Franzen, and G. Wittig, "Trimethylammonium‐methylid als Methylen‐Donator", Angewandte Chemie, vol. 72, pp. 417-417, 1960. https://doi.org/10.1002/ange.19600721210
  3. G. Wittig, and D. Krauss, "Cyclopropanierungen bei Einwirkung von <i>N</i>‐Yliden auf Olefine", Justus Liebigs Annalen der Chemie, vol. 679, pp. 34-41, 1964. https://doi.org/10.1002/jlac.19646790106
  4. H.S. Rzepa, "C 4 H 9 F 3 Li 1 N 1 O 3 S 1", 2015. https://doi.org/10.14469/ch/191545
  5. H.S. Rzepa, "C 5 H 11 F 3 Li 1 N 1 O 3 S 1", 2015. https://doi.org/10.14469/ch/191553
  6. H.S. Rzepa, and H.S. Rzepa, "C 5 H 17 F 3 Li 1 N 1 Ni 1 O 3 P 2 S 1", 2015. https://doi.org/10.14469/ch/191554
  7. H.S. Rzepa, "C 5 H 17 F 3 Li 1 N 1 Ni 1 O 3 P 2 S 1", 2015. https://doi.org/10.14469/ch/191536
  8. H.S. Rzepa, "C5H17F3LiNNiO3P2S", 2015. https://doi.org/10.14469/ch/191550
  9. H.S. Rzepa, and H.S. Rzepa, "C 5 H 17 F 3 Li 1 N 1 Ni 1 O 3 P 2 S 1", 2015. https://doi.org/10.14469/ch/191555
  10. H.S. Rzepa, "C 3 H 12 Ni 1 P 2", 2015. https://doi.org/10.14469/ch/191547
  11. H.S. Rzepa, "C3H12NiP2", 2015. https://doi.org/10.14469/ch/191546
  12. H.S. Rzepa, "C 3 H 12 Ni 1 P 2", 2015. https://doi.org/10.14469/ch/191541
  13. H.S. Rzepa, "C 3 H 12 Ni 1 P 2", 2015. https://doi.org/10.14469/ch/191540
  14. H.S. Rzepa, "C3H12NiP2", 2015. https://doi.org/10.14469/ch/191548
  15. H.S. Rzepa, "C 3 H 12 Ni 1 P 2", 2015. https://doi.org/10.14469/ch/191542
  16. H.S. Rzepa, "C 3 H 12 Ni 1 P 2", 2015. https://doi.org/10.14469/ch/191537
  17. H.S. Rzepa, "C3H12NiP2", 2015. https://doi.org/10.14469/ch/191538
  18. Buchalski, P.., Grabowska, I.., Kaminska, E.., and Suwinska, K.., "CCDC 650794: Experimental Crystal Structure Determination", 2008. https://doi.org/10.5517/ccpv6c2
  19. P. Buchalski, I. Grabowska, E. Kamińska, and K. Suwińska, "Synthesis and Structures of 9-Nickelafluorenyllithium Complexes", Organometallics, vol. 27, pp. 2346-2349, 2008. https://doi.org/10.1021/om701275u

Tags:, , , ,
Posted in Interesting chemistry, reaction mechanism | No Comments »