Posts Tagged ‘chemical education’

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

Enantioselective epoxidation of alkenes using the Shi Fructose-based catalyst. An undergraduate experiment.

Tuesday, April 15th, 2014

The journal of chemical education can be a fertile source of ideas for undergraduate student experiments. Take this procedure for asymmetric epoxidation of an alkene.[1] When I first spotted it, I thought not only would it be interesting to do in the lab, but could be extended by incorporating some modern computational aspects as well. 

Fructose

Oxygen atom transfer from this chiral dioxirane produces a specific enantiomer of the chiral epoxide in often high enantiomeric excess. For each alkene, there are up to eight possible transition states, arising from the following permutations:

  1. The two oxygen atoms of the oxidant are not equivalent
  2. Either the re or the si face of the alkene can be presented to the oxidant
  3. and the alkene itself can orient endo or exo with respect to the oxidant.

In fact, using the standard ωB97XD/6-311G(d,p)/SCRF=solvent method used on this blog, locating each transition state for any specific alkene can take about 24 hours, and hence doing all eight can take a week or more per alkene. We have groups of around 20 students doing this experiment, and so it was not practical in terms of computing resources to get them all to individually find these transition states. Instead, we give the students access to groups of eight pre-run calculations[2] for four different alkenes and invited them to perform various tasks for their selected alkene. These include: 

  1. Identify the free energy of each of the eight transition states for their alkene, and using these suggest a predicted enantiomeric outcome for the epoxide
  2. Using the energy of the lowest transition state leading to the other enantiomer, work out a predicted enantiomeric excess for the reaction
  3. Produce a non-covalent-interactions isosurface and try to reconcile this with the predicted ee by visual inspection.
  4. Run a QTAIM analysis of the wavefunction for the optimal transition state to inspect various topological critical points, especially the weaker ones that are not normally considered.
  5. Ponder any anomeric or other stereoelectronic interactions that might be present in any selected transition state.
  6. Track down the crystal structures of the catalyst precursor itself (the ketone) and comment on any interesting aspect of its structure.

There are more tasks the students have to perform, and a full description will appear in an article I am writing.

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References

  1. A. Burke, P. Dillon, K. Martin, and T.W. Hanks, "Catalytic Asymmetric Epoxidation Using a Fructose-Derived Catalyst", Journal of Chemical Education, vol. 77, pp. 271, 2000. https://doi.org/10.1021/ed077p271
  2. H.S. Rzepa, Mii Hii., and E.H. Smith, "Asymmetric epoxidation: a twinned laboratory and molecular modelling experiment", 2014. https://doi.org/10.6084/m9.figshare.988346

Enantioselective epoxidation of alkenes using the Shi Fructose-based catalyst. An undergraduate experiment.

Tuesday, April 15th, 2014

The journal of chemical education can be a fertile source of ideas for undergraduate student experiments. Take this procedure for asymmetric epoxidation of an alkene.[1] When I first spotted it, I thought not only would it be interesting to do in the lab, but could be extended by incorporating some modern computational aspects as well. 

Fructose

Oxygen atom transfer from this chiral dioxirane produces a specific enantiomer of the chiral epoxide in often high enantiomeric excess. For each alkene, there are up to eight possible transition states, arising from the following permutations:

  1. The two oxygen atoms of the oxidant are not equivalent
  2. Either the re or the si face of the alkene can be presented to the oxidant
  3. and the alkene itself can orient endo or exo with respect to the oxidant.

In fact, using the standard ωB97XD/6-311G(d,p)/SCRF=solvent method used on this blog, locating each transition state for any specific alkene can take about 24 hours, and hence doing all eight can take a week or more per alkene. We have groups of around 20 students doing this experiment, and so it was not practical in terms of computing resources to get them all to individually find these transition states. Instead, we give the students access to groups of eight pre-run calculations[2] for four different alkenes and invited them to perform various tasks for their selected alkene. These include: 

  1. Identify the free energy of each of the eight transition states for their alkene, and using these suggest a predicted enantiomeric outcome for the epoxide
  2. Using the energy of the lowest transition state leading to the other enantiomer, work out a predicted enantiomeric excess for the reaction
  3. Produce a non-covalent-interactions isosurface and try to reconcile this with the predicted ee by visual inspection.
  4. Run a QTAIM analysis of the wavefunction for the optimal transition state to inspect various topological critical points, especially the weaker ones that are not normally considered.
  5. Ponder any anomeric or other stereoelectronic interactions that might be present in any selected transition state.
  6. Track down the crystal structures of the catalyst precursor itself (the ketone) and comment on any interesting aspect of its structure.

There are more tasks the students have to perform, and a full description will appear in an article I am writing.

<

p>

References

  1. A. Burke, P. Dillon, K. Martin, and T.W. Hanks, "Catalytic Asymmetric Epoxidation Using a Fructose-Derived Catalyst", Journal of Chemical Education, vol. 77, pp. 271, 2000. https://doi.org/10.1021/ed077p271
  2. H.S. Rzepa, Mii Hii., and E.H. Smith, "Asymmetric epoxidation: a twinned laboratory and molecular modelling experiment", 2014. https://doi.org/10.6084/m9.figshare.988346