Posts Tagged ‘New Hampshire’

Fine-tuning a (hydrogen) bond into symmetry.

Friday, January 23rd, 2015

Sometimes you come across a bond in chemistry that just shouts at you. This happened to me in 1989[1] with the molecule shown below. Here is its story and, 26 years later, how I responded.

JAZCOC

To start at the beginning, there was a problem with the measured 1H NMR spectrum; specifically (Y=H, Z=O) there are supposedly 16 protons, but only 15 could be located. What had happened to the 16th? To understand how one proton had been “lost”, you should appreciate that on most FT-NMR instruments, one has to specify a spectral window to collect data, and normally for protons, that window ranges from ~14 to -2 ppm. So the standard response to lost signals is to expand the window. When that was done, the offending proton appeared at 19 ppm! You should understand that this is an unusual chemical shift for a proton, and is normally taken as indicating very high acidity. But carboxylic acid protons are not regarded as particularly acidic? The mystery was resolved by recording the crystal structure at low temperatures, and this revealed that this hydrogen was (almost) symmetrically disposed between the oxygen and the nitrogen. The N-H distance was 1.32Å and the OH 1.17Å. Whilst such symmetric disposition is not that unusual between two atoms of the same type (O-H-O or N-H-N) it was quite unexpected between two different heteroatoms. And such symmetry alone is sufficient to induce very high chemical shifts; acidity per se does not come into it.

That bond clearly shouted at me; so much so that in the text of the original article, we wrote “it is interesting to speculate whether these characteristics could be fine tuned by modification of the pKa values with suitable ring substitution“. What I had in mind was whether the position of the H could be made perfectly symmetric by adjusting the substituents. But for 26 years this idea lay dormant. Until this post! Rather than make lot of compounds (1-3 years!) I will do it with (lots of) computation (2 days!!).

So to start we need a reality check. I am using the pbe1pbe/tzvp/scrf=chloroform method (this functional is often used for hydrogen bonds) and the collected results are shown in the table below.

  1. For Y=H, Z=O, the calculation predicts single minimum, with the hydrogen closer to O. Starting from an NH bound hydrogen ends with it on O. It is what is called a single well potential. The disposition of that H is not quite correct, but the computed 1H NMR shift is pretty close to experiment, and so I will take this method as reasonably good.
  2. With Y=Li, the polarisation of the N-Li bond enhances the basicity of the second N, and the H now ends up on this atom rather than O (even if it starts on O). Another single well potential. We now know that any symmetric species must occur somewhere between Y=H and Y=Li in terms of the electronegativity of the substituent Y.
  3. Unsurprisingly, Y=Na does not bracket Y=H/Li and the H moves even closer to the N. Again a single well potential.
  4. Y=Li.1H2O or 2H2O do not help either (surprisingly?)
  5. Y=BeH brackets Y=H/Li, but we also see new behaviour with a double-well potential; the H can be attached to either O or N and the former is slightly more stable by 0.22 kcal/mol in ΔG. The barrier is tiny, well below the energy of the first vibrational level, and so experimentally this system will manifest as the average of these two isomers and the H will similarly manifest with its most probable position being at the average of the two minima, N-H ~1.30, O-H ~1.3Å. Success!  At this point, the NMR shift is at its greatest.
  6. Y=BH2 continues the trend as a double minimum, this time with the H-O species the more stable by ΔG 0.68 kcal/mol; we are now past the symmetric point.
  7. By Y=SiH3, the single-well minimum (with H-O) is restored and we emerge with the same result as Y=H.
  8. And to complete the scan, Y=H, Z=S is the same as Z=O.
  9. Some second order tuning can be tried by changing the substituent on Y=BeH to Y=BeF, again a double minimum with HO more stable than NH by 0.30 kcal/mol in ΔG, and with a ΔG298 barrier from O to N of only 0.02 kcal/mol! The fine-tuning is again towards symmetrisation.

I will stop at that point. Unfortunately of course the Y=BeF derivative is unfeasible synthetically and hence unlikely to be tested.

Y N-H, Å O-H, Å δ, ppm FAIR Data Citation
H (expt) 1.32 1.17 19.0 [1]
H (calc) 1.48 1.04 18.6 [2]
Li 1.06 1.52 16.5 [2]
Na 1.05 1.55 15.6 [3]
Li.H2O 1.06 1.52 16.6 [4]
Li.2H2O 1.06 1.52 16.6 [5]
BeH 1.11 1.39 20.6 [6]
BeH 1.49 1.04 18.7 [7]
BH2 1.06 1.56 16.6 [8]
BH2 1.53 1.03 17.6 [7]
SiH3 1.48 1.04 18.8 [9]
Z=S 1.50 1.03 18.8 [10]
BeF 1.12 1.38 20.9 [11]
BeF (TS) 1.15 1.32 22.5 [12]
BeF 1.48 1.04 18.7 [13]

Another reality check, a search of crystal structures. DIST2 = OH, DIST1 = NH, for structures recorded below 140K, R < 0.05%, no errors, no disorder. The structure above is shown as a blue dot. They do tend to show asymmetry, but it is interesting how many such structures have emerged since our own 1989 report; the effect is not that rare any more.
H-bond

The above plot shows lots more systems that might be subjected to the sort of tuning above, and who knows one of them may even yield to experimental validation.

References

  1. P. Camilleri, C.A. Marby, B. Odell, H.S. Rzepa, R.N. Sheppard, J.J.P. Stewart, and D.J. Williams, "X-Ray crystallographic and NMR evidence for a uniquely strong OH ? N hydrogen bond in the solid state and solution", Journal of the Chemical Society, Chemical Communications, pp. 1722, 1989. https://doi.org/10.1039/c39890001722
  2. H.S. Rzepa, "C 13 H 14 Li 1 N 3 O 3", 2015. https://doi.org/10.14469/ch/189475
  3. H.S. Rzepa, "C 13 H 14 N 3 Na 1 O 3", 2015. https://doi.org/10.14469/ch/189477
  4. H.S. Rzepa, "C 13 H 16 Li 1 N 3 O 4", 2015. https://doi.org/10.14469/ch/189478
  5. H.S. Rzepa, "C 13 H 18 Li 1 N 3 O 5", 2015. https://doi.org/10.14469/ch/189480
  6. H.S. Rzepa, "C 13 H 15 Be 1 N 3 O 3", 2015. https://doi.org/10.14469/ch/189476
  7. H.S. Rzepa, "C 13 H 15 Be 1 N 3 O 3", 2015. https://doi.org/10.14469/ch/189492
  8. H.S. Rzepa, "C 13 H 16 B 1 N 3 O 3", 2015. https://doi.org/10.14469/ch/189479
  9. H.S. Rzepa, "C 13 H 17 N 3 O 3 Si 1", 2015. https://doi.org/10.14469/ch/189481
  10. J.S. Dawson, "Cl 4 Ni 1 -2", 2016. https://doi.org/10.14469/ch/193726
  11. H.S. Rzepa, "C 13 H 14 Be 1 F 1 N 3 O 3", 2015. https://doi.org/10.14469/ch/189489
  12. C. Townsend, "Cl 4 Ni 1 -2", 2016. https://doi.org/10.14469/ch/193727

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Why diphenyl peroxide does not exist.

Monday, April 29th, 2013

A few posts back, I explored the “benzidine rearrangement” of diphenyl hydrazine. This reaction requires diprotonation to proceed readily, but we then discovered that replacing one NH by an O as in N,O-diphenyl hydroxylamine required only monoprotonation to undergo an equivalent facile rearrangement. So replacing both NHs by O to form diphenyl peroxide (Ph-O-O-Ph) completes this homologous series. I had speculated that PhNHOPh might exist if all traces of catalytic acid were removed, but could the same be done to PhOOPh? Not if it continues the trend and requires no prior protonation at all!

PhOOPh

Here is the results of a ωB97XD/6-311G(d,p)/SCRF=water calculation. Now I should explain that the conventional explanation for the non-existence of PhOOPh is that the O-O bond homolyses very readily to form phenoxy radicals[1]. But of course other peroxides such as t-Bu-O-O-t-Bu do exist (although they are rather fragile) and so the phenyl analogue is clearly special.

PhOOPh  PhOOPha1 
 PhOOPh2 PhOOPha1 

You will notice from the IRC profiles shown above that even without any prior protonation, the barrier to O-O cleavage is really very small (~ 4 kcal/mol). But the method I have used to calculate this is a closed shell DFT procedure. This does not allow the formation of the (open shell) biradical that two phenoxy radicals would represent. The barrier is low even without the formation of phenoxy radicals! Of course, as with the two previous examples, the actual initial product formed is the π-complex as first suggested by Michael Dewar. The wavefunction of such a species requires special treatment, since it is best described as a linear combination of two closed-shell configurations, what is called a multi-configuration or multi-reference wavefunction.‡ So the single-configuration closed shell calculation that the above IRC represents must be an upper bound to a proper description of the energy transition state. In other words, if the description is improved, the barrier can only get even lower! 

Notice in the above that the π-complex formed in the first stage (of two) is actually lower in energy than the diphenyl peroxide itself, and that the barrier for this π-complex to then collapse to form the C-C bond between the two 4-positions is also tiny. This π-complex in other words is very transient indeed, probably not surviving for even one molecular vibration. To all intents and purposes, this really is a concerted [5,5] sigmatropic shift, as shown in the schematic at the top of this post. But the bottom line is that the homolysis argument need not be the only one (although it  is not necessarily incorrect). One can just as readily explain why PhOOPh does not exist by invoking facile formation of Dewar-like π-complex instead.

‡ Another deceptively simple little molecule that requires such a treatment is C2, the topic of much recent debate![2], [3]

References

  1. R. Benassi, U. Folli, S. Sbardellati, and F. Taddei, "Conformational properties and homolytic bond cleavage of organic peroxides. I. An empirical approach based upon molecular mechanics and <i>ab initio</i> calculations", Journal of Computational Chemistry, vol. 14, pp. 379-391, 1993. https://doi.org/10.1002/jcc.540140402
  2. S. Shaik, H.S. Rzepa, and R. Hoffmann, "One Molecule, Two Atoms, Three Views, Four Bonds?", Angewandte Chemie International Edition, vol. 52, pp. 3020-3033, 2013. https://doi.org/10.1002/anie.201208206
  3. J.M. Matxain, F. Ruipérez, I. Infante, X. Lopez, J.M. Ugalde, G. Merino, and M. Piris, "Communication: Chemical bonding in carbon dimer isovalent series from the natural orbital functional theory perspective", The Journal of Chemical Physics, vol. 138, 2013. https://doi.org/10.1063/1.4802585

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