Posts Tagged ‘Dieter Cremer’

WATOC 2017 report.

Tuesday, August 29th, 2017

The triennial conference is this year located in Munich. With 1500 participants and six parallel sessions, this report can give only a flavour of proceedings.

  1. Edward Valeev talked about the scaling problem in coupled cluster theories, the so-called gold standard for computing the energy and properties of small molecules. The problem is that the number of basis functions N describing the atomic basis set for the atoms scales from between N6 to N10 in terms of computer time, with similar behaviour for the memory required for the calculation. He described methods based on natural pair orbitals and localisation schemes which can achieve linear scaling, ie N1 for the energy, quite a break through! Using reasonable basis sets, CCSD(T)-like energies for molecules with 100s of atoms were reported. During the Q&A time afterwards (the tight schedules associated with so many speakers means questions are often limited to 1-2, with very short answers) a question was posed about the prospects for first and second derivatives for the method. This means that e.g. reaction mechanisms can then be probed with unprecedented energetic accuracy. The answer was non-committal, but if these derivatives do arrive, it will revolutionise our ability to understand mechanisms.
  2. Which brings me nicely to Jeremy Harvey, who talked about calculating accurate overall rate constants for complex mechanistic cycles. The rate equations are solved for the steady state condition and include concentrations of all species and the energies are obtained using CCSD(T)-F12 theory (a modification which allows better basis set scaling without increased computation time) as single point geometries. He described an example where the barrier associated with a postulated mechanism was about 6 kcal/mol higher than derived from the observed rate. This was sufficient to induce them to explore alternative mechanisms, which were indeed located with an appropriately lower barrier. I have used the value of ~10 kcal/mol as my mechanistic test on this blog, and it’s really nice to see this value being reduced further.
  3. Yet again this theme emerged with Yitzhak Apeloig, who asked about the mechanism for C=Si bond rotations in substituted systems recently made in his group. The energy of this rotation is low enough to be observed in NMR spectra. But when the energy of C=Si bond rotation is computed it comes out about 10 kcal/mol too high. Again alternative mechanisms were explored and it turns out that a 1,2 migration from R2C=SiR2 to form a carbylidene species, R-C-SiR3, rotation and then 1,2 again to reformulate the R2C=SiR2 system came up with the goods.
  4. Peter Scheiner talked about how attractions between molecules can be induced by dispersion. He described how Ph3C-CPh3 is an unknown molecule (dissociating into Ph3P radicals) but when 4,6-di-tert-butyl groups are placed on all the phenyl rings, the dispersion attractions between them can account for ~60 kcal/mol (!), more than enough to stabilise the system. I have already described some of this work in a post here. The prospects are very exciting for more dispersion-stabilised molecules to emerge. During Q&A, a question was posed about what other atom pairs other than H…H might be brought into ultra-short contact by these attractive dispersion forces; we may expect further examples to emerge in the near future.
  5. Ken Houk gave a fascinating glimpse into the post-transition state world of reaction dynamics, as applied to Diels Alder cycloadditions and Cope rearrangements. The reactions are characterised by the residency times of the dynamic trajectories in the region of the transition state as short (~4 fs), medium (20-40fs) and long (80+fs), these times mapping on to what we used to call “synchronous”, “asynchronous” and “stepwise”. A good example is the so-called bis-pericyclic reaction of cyclopentadiene where the trajectories pass through a transition state but then bifurcate into two (in this case) equivalent pathways. He discussed other examples where the trajectories follow either a 2+4 cycloaddition pathway or a 4+6 alternative pathway and how the number of trajectories for each can be influenced by either solvent (water) or an enzyme. Ken described several 20-40fs trajectories as corresponding to “dynamic stepwise” reactions, which during Q&A was suggested are equivalent to the term “hidden intermediate” pathways coined by Dieter Cremer and as revealed in many posts here from the intrinsic reaction coordinates or IRCs. This is a clear growth area and expect many more examples of reaction dynamics to be applied to many exciting systems in the future.
  6. Leo Radom talked about very simple molecules, H3CX and the effects on the bond dissociation energy (BDE) of the C-H bonds if the group X is either strongly or weakly protonated (the latter via a hydrogen bond), or deprotonated (again strongly or weakly via a hydrogen bond from hydroxide anion). This is important in several enzymic pathways, where the CH bond might be activated in a similar manner by the enzyme. He also talked about similar effects on the ionisation potential. I noticed a connection between this theme and what might be called the electron affinity of H3CX. If you want to see what the connection is, go visit the Aachen bond Slam, about which I have previously blogged! 

I will stop with an observation that all the notes above were taken in real-time during the talks, which all emerged as Powerpoint slides, having an average residency time on the screen of perhaps 1-2 minutes each. References were invariably given as full journal citations (authors, journal, year, volume, pages) rather than as DOIs, and given the time constraints I did not try to capture them. Hence the lack of citations above to the presenters’ work. The slide displays are traditionally not made available to audiences and photography of the screen or recording is considered very bad form. Conferences are not really about FAIR data, which I have described often on this blog.

I hope these six examples give one flavour of what is happening at WATOC 2017. If another interesting collection emerges, I may describe it here.


But see e.g. doi: b9r9 for an Aachen talk.

Experimental evidence for “hidden intermediates”? Epoxidation of ethene by peracid.

Sunday, August 25th, 2013

The concept of a “hidden intermediate” in a reaction pathway has been promoted by Dieter Cremer[1] and much invoked on this blog. When I used this term in a recent article of ours[2], a referee tried to object, saying it was not in common use in chemistry. The term clearly has an image problem. A colleague recently sent me an article to read (thanks Chris!) about isotope effects in the epoxidation of ethene[3] and there I discovered a nice example of hidden intermediates which I share with you now.

peracid

The reaction above is considered as a transfer of an oxygen atom to an alkene with concomitant concerted proton transfer (for the analogous reaction of an alkyne see here). The mechanism is normally illustrated with five arrows accomplishing both operations (see below). But a simple experiment shows this cannot be accurate[3]. When d4-ethene is used (with mCPBA as the peracid) in dichloromethane solution, an inverse kinetic isotope effect of 0.83 is observed (in other words the d4– species reacts faster than the 1H). If the peracid is instead deuterated (as OD) the reaction slows down by a factor of 1.05 (a normal isotope effect). This data provides a good test of whether any transition state model constructed for the reaction is a good one. So how about a ωB97XD/6-311G(d,p)/SCRF=dichloromethane[4],[5] model, using per-ethanoic acid? The isotope effect can be obtained by calculating the activation free energy with the appropriate isotope specified.

Activation barriers for isotopic substitutions
Value Normal isotopes d4-ethene OD acid One 13C-ethene One 18O
ΔG298 26.6844375 26.5589375 26.7245975 26.6907125 26.7296175
KIE  – 0.808 1.070 1.011 1.080

The deuterium isotope effects, on both carbon and oxygen compare very well indeed with those measured (the 13C and 18O have never been measured, they are predictions), which greatly assures that the model is a good one. So the predicted transition state geometry as shown below has had a good reality check. It reveals that two O-C bonds are forming, and the O-O bond is breaking, but that proton transfer has hardly started. This corresponds to the three green arrows shown at the top. The three blue arrows are not yet in action. I have colour-coded them to illustrate this temporal aspect. 

peracid+alkene1

An intrinsic reaction coordinate[6] shows that the reaction is concerted, albeit asynchronous; the transition state (TS, @IRC=0.0) really only involves the green arrows; the blue arrows kick in only AFTER the ion-pair-like hidden intermediate is formed, labelled HI above (and seen @IRC =+1.2). Stabilising the ion-pair using trifluorethanoic acid[7] (a stronger acid) renders the HI more prominent.

peracid
peracidG
peracidF
peracidFG

As quantum calculations apparently give us trustworthy indications of the order in which events happen during this reaction mechanism, perhaps it is time to start representing this information in our simple schematics. (Some) text-books currently show the left hand diagram below, involving five arrows but with no indication of their relative timing. The right hand side now colours the arrows to indicate that the green precede the blue. An extra arrow is added to indicate that one electron pair is involved in forming a “hidden intermediate”, the green arrow aspiring to end at a lone pair, but the blue arrow then continuing its progress to the final epoxide. The end-point of one arrow representing the start point of another could thus be taken as implying a hidden intermediate.

peracid1

As I have noted elsewhere, the curly-arrow representation of reaction mechanism has hardly evolved over the last sixty years. Some might argue that such stability is appropriate for a very simple heuristic used to teach introductory chemistry to students, and that this very simplicity should not be gratuitously discarded. But perhaps, in the light of what we now know about many mechanisms, it has become over-simple? Could judiciously deployed colour-coding of the arrows be a useful, albeit perhaps only a small step, to upgrading arrow pushing into the 21st century? 


I appreciate that some people are red-green/blue-yellow colour-blind, and that a full ROYGBIV spectrum of colours may carry too much information!

References

  1. E. Kraka, and D. Cremer, "Computational Analysis of the Mechanism of Chemical Reactions in Terms of Reaction Phases: Hidden Intermediates and Hidden Transition States", Accounts of Chemical Research, vol. 43, pp. 591-601, 2010. https://doi.org/10.1021/ar900013p
  2. H.S. Rzepa, and C. Wentrup, "Mechanistic Diversity in Thermal Fragmentation Reactions: A Computational Exploration of CO and CO<sub>2</sub> Extrusions from Five-Membered Rings", The Journal of Organic Chemistry, vol. 78, pp. 7565-7574, 2013. https://doi.org/10.1021/jo401146k
  3. T. Koerner, H. Slebocka-Tilk, and R.S. Brown, "Experimental Investigation of the Primary and Secondary Deuterium Kinetic Isotope Effects for Epoxidation of Alkenes and Ethylene with <i>m</i>-Chloroperoxybenzoic Acid", The Journal of Organic Chemistry, vol. 64, pp. 196-201, 1998. https://doi.org/10.1021/jo981652x
  4. H.S. Rzepa, "Gaussian Job Archive for C4H8O3", 2013. https://doi.org/10.6084/m9.figshare.781238
  5. H.S. Rzepa, "Gaussian Job Archive for C4H8O3", 2013. https://doi.org/10.6084/m9.figshare.781284
  6. H.S. Rzepa, "Gaussian Job Archive for C4H5F3O3", 2013. https://doi.org/10.6084/m9.figshare.781283

Experimental evidence for "hidden intermediates"? Epoxidation of ethene by peracid.

Sunday, August 25th, 2013

The concept of a “hidden intermediate” in a reaction pathway has been promoted by Dieter Cremer[1] and much invoked on this blog. When I used this term in a recent article of ours[2], a referee tried to object, saying it was not in common use in chemistry. The term clearly has an image problem. A colleague recently sent me an article to read (thanks Chris!) about isotope effects in the epoxidation of ethene[3] and there I discovered a nice example of hidden intermediates which I share with you now.

peracid

The reaction above is considered as a transfer of an oxygen atom to an alkene with concomitant concerted proton transfer (for the analogous reaction of an alkyne see here). The mechanism is normally illustrated with five arrows accomplishing both operations (see below). But a simple experiment shows this cannot be accurate[3]. When d4-ethene is used (with mCPBA as the peracid) in dichloromethane solution, an inverse kinetic isotope effect of 0.83 is observed (in other words the d4– species reacts faster than the 1H). If the peracid is instead deuterated (as OD) the reaction slows down by a factor of 1.05 (a normal isotope effect). This data provides a good test of whether any transition state model constructed for the reaction is a good one. So how about a ωB97XD/6-311G(d,p)/SCRF=dichloromethane[4],[5] model, using per-ethanoic acid? The isotope effect can be obtained by calculating the activation free energy with the appropriate isotope specified.

Activation barriers for isotopic substitutions
Value Normal isotopes d4-ethene OD acid One 13C-ethene One 18O
ΔG298 26.6844375 26.5589375 26.7245975 26.6907125 26.7296175
KIE  – 0.808 1.070 1.011 1.080

The deuterium isotope effects, on both carbon and oxygen compare very well indeed with those measured (the 13C and 18O have never been measured, they are predictions), which greatly assures that the model is a good one. So the predicted transition state geometry as shown below has had a good reality check. It reveals that two O-C bonds are forming, and the O-O bond is breaking, but that proton transfer has hardly started. This corresponds to the three green arrows shown at the top. The three blue arrows are not yet in action. I have colour-coded them to illustrate this temporal aspect. 

peracid+alkene1

An intrinsic reaction coordinate[6] shows that the reaction is concerted, albeit asynchronous; the transition state (TS, @IRC=0.0) really only involves the green arrows; the blue arrows kick in only AFTER the ion-pair-like hidden intermediate is formed, labelled HI above (and seen @IRC =+1.2). Stabilising the ion-pair using trifluorethanoic acid[7] (a stronger acid) renders the HI more prominent.

peracid
peracidG
peracidF
peracidFG

As quantum calculations apparently give us trustworthy indications of the order in which events happen during this reaction mechanism, perhaps it is time to start representing this information in our simple schematics. (Some) text-books currently show the left hand diagram below, involving five arrows but with no indication of their relative timing. The right hand side now colours the arrows to indicate that the green precede the blue. An extra arrow is added to indicate that one electron pair is involved in forming a “hidden intermediate”, the green arrow aspiring to end at a lone pair, but the blue arrow then continuing its progress to the final epoxide. The end-point of one arrow representing the start point of another could thus be taken as implying a hidden intermediate.

peracid1

As I have noted elsewhere, the curly-arrow representation of reaction mechanism has hardly evolved over the last sixty years. Some might argue that such stability is appropriate for a very simple heuristic used to teach introductory chemistry to students, and that this very simplicity should not be gratuitously discarded. But perhaps, in the light of what we now know about many mechanisms, it has become over-simple? Could judiciously deployed colour-coding of the arrows be a useful, albeit perhaps only a small step, to upgrading arrow pushing into the 21st century? 


I appreciate that some people are red-green/blue-yellow colour-blind, and that a full ROYGBIV spectrum of colours may carry too much information!

References

  1. E. Kraka, and D. Cremer, "Computational Analysis of the Mechanism of Chemical Reactions in Terms of Reaction Phases: Hidden Intermediates and Hidden Transition States", Accounts of Chemical Research, vol. 43, pp. 591-601, 2010. https://doi.org/10.1021/ar900013p
  2. H.S. Rzepa, and C. Wentrup, "Mechanistic Diversity in Thermal Fragmentation Reactions: A Computational Exploration of CO and CO<sub>2</sub> Extrusions from Five-Membered Rings", The Journal of Organic Chemistry, vol. 78, pp. 7565-7574, 2013. https://doi.org/10.1021/jo401146k
  3. T. Koerner, H. Slebocka-Tilk, and R.S. Brown, "Experimental Investigation of the Primary and Secondary Deuterium Kinetic Isotope Effects for Epoxidation of Alkenes and Ethylene with <i>m</i>-Chloroperoxybenzoic Acid", The Journal of Organic Chemistry, vol. 64, pp. 196-201, 1998. https://doi.org/10.1021/jo981652x
  4. H.S. Rzepa, "Gaussian Job Archive for C4H8O3", 2013. https://doi.org/10.6084/m9.figshare.781238
  5. H.S. Rzepa, "Gaussian Job Archive for C4H8O3", 2013. https://doi.org/10.6084/m9.figshare.781284
  6. H.S. Rzepa, "Gaussian Job Archive for C4H5F3O3", 2013. https://doi.org/10.6084/m9.figshare.781283