Posts Tagged ‘calculated free energy’

Mechanism of the solvatochromic reaction of a spiropyran.

Wednesday, February 4th, 2015

The journal of chemical education has many little gems providing inspiration for laboratory experiments. Jonathan Piard reports one based on the reaction below[1]; here I investigate the mechanism of this transformation.

spiropyran
There are two things going on here; an electrocyclic ring opening involving breaking the C-O bond, with a cis/trans isomerism of the alkene (concurrent or consecutive). A crystal structure of the dinitro analogue establishes the trans stereochemistry[2]. This product zwitterion is highly coloured (blue-purple) unlike the colourless reactant. The rate at which this colour clears can be easily measured in a UV/visible spectrometer, and from this activation parameters are inferred as a function of the solvent.

Photochemically, this reaction is too complex to study quickly using computation, but the thermal back reaction is much easier. Applying the ωB97XD/6-311G(d,p)/SCRF=solvent procedure and using the C-O bond as a reaction coordinate results in the following transition state[3] IRC profile[4] for DMSO as solvent, here connecting to the cis-alkene. The thermal forward barrier for the C…O cleaving is ~12 kcal/mol. More significantly, the back reaction is only <2 kcal mol, which is very much lower than that reported[1] (~22 kcal/mol) and makes the cis-alkene very much a transient species and therefore not the coloured species being measured.

C-O-cleave

A second transition state involving C=C bond rotation is located[5] and this yields the following IRC[6] to form the trans-alkene, with activation parameters listed below. It is entirely probable however that the forward photochemical reaction follows a different course involving conical intersections; an interesting study in its own right, but beyond the scope of this post.

cis-trans

Measured and computed activation parameters for the thermal back reaction
Solvent ΔG298, kcal mol-1 ΔH, kcal mol-1 ΔS, cal K-1 mol-1
DMSO, measured 22.0 26.4 +14.6
toluene, measured 19.0 14.3 -15.6
DMSO, calc[5] 21.2 20.4 +2.6
toluene, calc[7] 18.6 19.1 +1.8

The next issue surrounds the effect of solvent. Most spectacular are those of the activation parameters for the thermal back-reaction. The measured activation entropy ΔS changes with solvent by Δ30.2 cal, and the enthalpy ΔH by Δ12.1 kcal, which are enormous solvent effects. Are they in fact real? It is reassuring at least that the calculated free energy agrees pretty closely with the measured values. So too does the decrease in ΔG in changing the solvent from DMSO to toluene (3.0 kcal/mol measured, 2.6 calculated).

There is little sign of a large solvent effect in the calculated values. This could be for three reasons.

  1. The first is that adding explicit, hydrogen-bonded solvent molecules to the system is essential. As the zwitterionic character is lost when the trans-alkene starts to rotate, the system will become less ionic, and hence shed solvent molecules and gain entropy. If the solvent is not capable of hydrogen bonding, as say toluene, these will not be shed and the entropy will not increase at the transition state. It is difficult however to reconcile this picture with the apparent large loss of entropy for toluene as solvent.
  2. The second reason is because of a complete change in mechanism, one not modelled here.
  3. For completeness, one should also mention that the measured values might simply be in error, either due to typographical mistakes or indeed in numerical analysis.

I will conclude with the colour. It is possible to compute the electronic excitations across the range 180-580nm, and I show below a difference spectrum (for DMSO as solvent) with the product +ve and the reactant  -ve. You can see the spectacular red-shift for the highly conjugated zwitterion! The absolute value of λmax is not red-shifted enough (by about 65 nm), but the effect remains real.
spiro

The above experiment is for undergraduate chemistry laboratories. I suggest that a computational reality check could also easily be included into such a lab, and would certainly help give students a broader perspective.

References

  1. J. Piard, "Influence of the Solvent on the Thermal Back Reaction of One Spiropyran", Journal of Chemical Education, vol. 91, pp. 2105-2111, 2014. https://doi.org/10.1021/ed4005003
  2. J. Hobley, V. Malatesta, R. Millini, L. Montanari, and W. O Neil Parker, Jr, "Proton exchange and isomerisation reactions of photochromic and reverse photochromic spiro-pyrans and their merocyanine forms", Physical Chemistry Chemical Physics, vol. 1, pp. 3259-3267, 1999. https://doi.org/10.1039/a902379h
  3. H.S. Rzepa, "C 19 H 18 N 2 O 3", 2015. https://doi.org/10.14469/ch/189540
  4. H.S. Rzepa, "C19H18N2O3", 2015. https://doi.org/10.14469/ch/189573
  5. H.S. Rzepa, "C 19 H 18 N 2 O 3", 2015. https://doi.org/10.14469/ch/189546
  6. H.S. Rzepa, "C19H18N2O3", 2015. https://doi.org/10.14469/ch/189648
  7. H.S. Rzepa, "C 19 H 18 N 2 O 3", 2015. https://doi.org/10.14469/ch/189579

The formation of cyanohydrins: re-writing the text books. ! or ?

Friday, March 4th, 2011

Nucleophilic addition of cyanide to a ketone or aldehyde is a standard reaction for introductory organic chemistry. But is all as it seems? The reaction is often represented as below, and this seems simple enough.

Cyanohydrin formation.

But attention to detail suggests that, HCN being a weak acid, there will be only a very small concentration of cyanide anion in the presence of HCl. There are other aspects which (if fussy) one might quibble with. The arrow pushing originates at the negative sign of the cyanide group. It is slightly more accurate to suggest that any arrow shown originates at an electron pair rather than necessarily a charge (think borohydride anion).

Possible sources of electron pairs in "HCN"

In cyanide anion, the relevant electron pair is shown above in red (a). But if most of this anion is really protonated in HCl, then the electron pair resides in a H-C bond (b). Or, if we put the proton on the nitrogen, then again it becomes a lone pair (c). So, can we formulate a mechanism for cyanohydrin formation for acidic solutions, which avoids the need to use (a)?

7-ring mechanism for cyanohydrin formation.

We need to borrow a water molecule, and then isomerise the HCN to HNC, before subjecting the combination to a cyclic reaction. Is this viable? To answer that, we will do a ωB97XD/6-311G(d,p)/SCRF=water calculation. Solvating this reaction with both (at least) one explicit water, and a continuum field model is crucial. The calculated free energy of activation for this process with respect to HCN+H2O+carbonyl is 30.0 kcal/mol. This is a bit high for a reaction that occurs readily at room temperatures, but perhaps with a better model which includes more explicit water molecules, it might be regarded as a reasonable alternative to the cyanide anion mechanism.

Transition state for cyanohydrin formation. Click for 3D

Are there any other possibilities? Well, one might be to protonate the carbonyl group first using that HCl. This might activate the carbonyl group towards nucleophilic attack (the Prins reaction), and hence make it more reactive. This counteracts the intrinsic low nucleophilicity of a H-C bond  (compared to e.g. a lone pair).

Alternative mechanism for cyanohydrin formation

This results in a 6-ring transition state with an activation free energy of 33.4 kcal/mol with respect to  HCN+H2O+protonated carbonyl. This transition state has a very unusual feature, namely water acting as a base removing the proton from HCN, and the same carbon that is losing this proton is also forming a new C-C bond to make the cyanohydrin. Such a bimolecular displacement at an sp-hybridized carbon centre is quite unusual (and it also happens with retention of “configuration” at the carbon, an SNi reaction). Notice also that the proton removal occurs as a linear geometry, and the carbon attacks the (protonated) carbonyl at 111°.

6-ring transition state. Click for 3D

What have we learnt? Well, that quite subtle alternatives to the text-book arrow pushing for the formation of a cyanohydrin are possible. There may be more which have not yet been located! These cyclic (or almost cyclic) mechanisms solve the problem of using cyanide anion in HCl solutions, and their predicted activation energies are not entirely unreasonable. Whilst the above do not represent a definitive answer to this mechanism, it does suggest that many a text-book diagram used by students may deserve a re-think, or at least a calculation!