Posts Tagged ‘Henry Rzepa’

Following one’s nose: a quadruple bond to carbon. Surely I must be joking!

Thursday, December 16th, 2010

Do you fancy a story going from simplicity to complexity, if not absurdity, in three easy steps? Read on! The following problem appears in one of our (past) examination questions in introductory organic chemistry. From relatively mundane beginnings, one can rapidly find oneself in very unexpected territory.

How would one make 3-nitrobenzonitrile?

One teaches how to disconnect each group, identifying that both are meta-directing towards electrophiles, and hence asking what an appropriate electrophile might be? The “correct” answer is a nitronium cation (nitric + sulfuric acids) acting upon m-directing benzonitrile. But (sacrilege), why not a “cyonium” cation (CN+) on m-directing nitrobenzene? Well, as a tutor one would normally swat it away on the grounds it has never been previously observed (or that cyanide is always seen as an anion, not a cation). But then one (or a student) asks, why not? How about generating it from e.g. TfOCN. TfO– is a jolly good leaving group, one of the best. Well, this precursor truly appears never to have been made (or even calculated!). By now (if encountered in a tutorial), most chemistry students would be rather bemused. So the process of following one’s nose (more accurately, my nose) continues in the peace and quiet of a blog, where a rather different readership might be bemused (or inflamed).

A Quadruple CN bond?

One might start the same place a student would. How would one represent this diatomic with bonds? How about the above? It has the merit that both atoms are associated with a (shared) octet of electrons, in the form of a quadruple bond. I did show this (briefly) to a colleague, but they recoiled in horror, although it has to be said they were slightly at a loss to actually explain their horror.

Well, time for calculations. How about CCSD/aug-cc-pVTZ (DOI: 10042/to-6261) or B3LYP/aug-cc-pVTZ (DOI: 10042/to-6255). The latter allows a so-called Wiberg bond index to be computed (a reasonably accepted index). This comes out at 3.55, well on the way to being quadruple. An NBO analysis (NBO 5.9) identifies FOUR NBO orbitals with an occupancy of ~2.0, all designated BD (rather than e.g. Lp). What are these NBOs like? (as it turns out, they are almost identical to the MOs for this molecule).

Orbital 7. Click for 3D

Orbital 6 (π)

Orbital 5 (π)

Orbital 4. Click for 3D

Orbital 3. Click for 3D

Orbitals 5 & 6 are standard π orbitals with no mystery (and 8 & 9, not shown, are the matching π* pair). Orbital 3 results from the overlap of two 2s AOs (but note the curious little toroid at the carbon end). Orbitals 4 and 7 (the LUMO) are the interesting ones. Nominally, the result of overlapping two 2px AOs to give what should be a bonding and antibonding pair, they both appear to be bonding in the C-N region! Perhaps the quadruple bond is not looking quite so unlikely after all (comprising ~double occupancy of orbitals  3-6)!

What about those stalwarts I often use in these blogs, QTAIM and ELF? The former  (using the CCSD natural orbitals) has a ρ(r) of 0.346 and a ∇2ρ(r) of +2.01 at the bond-critical point (BCP). The former is certainly a high value, although no calibration exists to compare it to a quadruple bond. The Laplacian has a positive value at this point, possibly an indication of a charge-shift bond (see this and this blog, although more likely due to the adjacency of the bond critical point to the core shell of the carbon atom). ELF (also using natural orbitals) declares the presence of TWO disynaptic basins, with integrations of 5.39e and 2.44 (totalling 7.83e). The basins will each take the form of a torus (see DOI: 10.1021/ct100470g). Hm, perhaps, on reflection, this paragraph might not be entirely suitable for an introductory tutorial to organic chemistry. The density of mumbo-jumbo is rather high!

So starting from a simple retrosynthetic analysis of a simple aromatic molecule, in which the less obvious route is at least considered, one derives a “new” reagent, the cyonium cation CN+. In a effort to analyse its bonding, one concludes that a quadruple bond needs to be taken at least seriously. I would note as a warning that these diatomic species can be really tricky to pin down, and the iso-electronc C2 is a good example of that. But C2 has all sorts of issues, some of which are avoided with CN+. So the last word is hardly written, but not a bad outcome, I venture to suggest, of following one’s nose in a tutorial.

I have appended to this post a 3D exploration of the ELF function, showing the two torus basins referred to above.

 

ELF function for CN+. Click for 3D

Henry Rzepa, URL:http://www.ch.imperial.ac.uk/rzepa/blog/?p=3065. Accessed: 2011-06-04. (Archived by WebCite® at http://www.webcitation.org/5zBSjBjhM)

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Posted in Hypervalency, Interesting chemistry | 19 Comments »

Following one's nose: a quadruple bond to carbon. Surely I must be joking!

Thursday, December 16th, 2010

Do you fancy a story going from simplicity to complexity, if not absurdity, in three easy steps? Read on! The following problem appears in one of our (past) examination questions in introductory organic chemistry. From relatively mundane beginnings, one can rapidly find oneself in very unexpected territory.

How would one make 3-nitrobenzonitrile?

One teaches how to disconnect each group, identifying that both are meta-directing towards electrophiles, and hence asking what an appropriate electrophile might be? The “correct” answer is a nitronium cation (nitric + sulfuric acids) acting upon m-directing benzonitrile. But (sacrilege), why not a “cyonium” cation (CN+) on m-directing nitrobenzene? Well, as a tutor one would normally swat it away on the grounds it has never been previously observed (or that cyanide is always seen as an anion, not a cation). But then one (or a student) asks, why not? How about generating it from e.g. TfOCN. TfO– is a jolly good leaving group, one of the best. Well, this precursor truly appears never to have been made (or even calculated!). By now (if encountered in a tutorial), most chemistry students would be rather bemused. So the process of following one’s nose (more accurately, my nose) continues in the peace and quiet of a blog, where a rather different readership might be bemused (or inflamed).

A Quadruple CN bond?

One might start the same place a student would. How would one represent this diatomic with bonds? How about the above? It has the merit that both atoms are associated with a (shared) octet of electrons, in the form of a quadruple bond. I did show this (briefly) to a colleague, but they recoiled in horror, although it has to be said they were slightly at a loss to actually explain their horror.

Well, time for calculations. How about CCSD/aug-cc-pVTZ (DOI: 10042/to-6261) or B3LYP/aug-cc-pVTZ (DOI: 10042/to-6255). The latter allows a so-called Wiberg bond index to be computed (a reasonably accepted index). This comes out at 3.55, well on the way to being quadruple. An NBO analysis (NBO 5.9) identifies FOUR NBO orbitals with an occupancy of ~2.0, all designated BD (rather than e.g. Lp). What are these NBOs like? (as it turns out, they are almost identical to the MOs for this molecule).

Orbital 7. Click for 3D

Orbital 6 (π)

Orbital 5 (π)

Orbital 4. Click for 3D

Orbital 3. Click for 3D

Orbitals 5 & 6 are standard π orbitals with no mystery (and 8 & 9, not shown, are the matching π* pair). Orbital 3 results from the overlap of two 2s AOs (but note the curious little toroid at the carbon end). Orbitals 4 and 7 (the LUMO) are the interesting ones. Nominally, the result of overlapping two 2px AOs to give what should be a bonding and antibonding pair, they both appear to be bonding in the C-N region! Perhaps the quadruple bond is not looking quite so unlikely after all (comprising ~double occupancy of orbitals  3-6)!

What about those stalwarts I often use in these blogs, QTAIM and ELF? The former  (using the CCSD natural orbitals) has a ρ(r) of 0.346 and a ∇2ρ(r) of +2.01 at the bond-critical point (BCP). The former is certainly a high value, although no calibration exists to compare it to a quadruple bond. The Laplacian has a positive value at this point, possibly an indication of a charge-shift bond (see this and this blog, although more likely due to the adjacency of the bond critical point to the core shell of the carbon atom). ELF (also using natural orbitals) declares the presence of TWO disynaptic basins, with integrations of 5.39e and 2.44 (totalling 7.83e). The basins will each take the form of a torus (see DOI: 10.1021/ct100470g). Hm, perhaps, on reflection, this paragraph might not be entirely suitable for an introductory tutorial to organic chemistry. The density of mumbo-jumbo is rather high!

So starting from a simple retrosynthetic analysis of a simple aromatic molecule, in which the less obvious route is at least considered, one derives a “new” reagent, the cyonium cation CN+. In a effort to analyse its bonding, one concludes that a quadruple bond needs to be taken at least seriously. I would note as a warning that these diatomic species can be really tricky to pin down, and the iso-electronc C2 is a good example of that. But C2 has all sorts of issues, some of which are avoided with CN+. So the last word is hardly written, but not a bad outcome, I venture to suggest, of following one’s nose in a tutorial.

I have appended to this post a 3D exploration of the ELF function, showing the two torus basins referred to above.

 

ELF function for CN+. Click for 3D

Henry Rzepa, URL:http://www.ch.imperial.ac.uk/rzepa/blog/?p=3065. Accessed: 2011-06-04. (Archived by WebCite® at http://www.webcitation.org/5zBSjBjhM)

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Posted in Hypervalency, Interesting chemistry | 15 Comments »

Janus mechanisms (the past and the future): Reactions of the diazonium cation.

Saturday, December 11th, 2010

Janus was the mythological Roman god depicted as having two heads facing opposite directions, looking simultaneously into the past and the future. Some of the most ancient (i.e. 19th century) known reactions can be considered part of a chemical mythology; perhaps it is time for a Janus-like look into their future.

Reaction of the diazonium cation with cyanide.

The phenyl diazonium ion is often introduced early in most chemistry teaching; it is used to produce spectacularly coloured solutions from colourless starting materials and makes an immediate impression.1 The reaction of this species with cyanide salts often appears in introductory courses of aromatic chemistry as a means of producing aryl cyanides. It entered the text books around a century ago as the Sandmeyer reaction (using copper(I)cyanide, but it is also reported as occurring using more ionic cyanide salts as well).2 The mechanism of the ionic reaction however has been given little attention recently. One common representation is as a unimolecular reaction to lose nitrogen gas forming an arene cation, which is mechanistically then followed by fast quenching with cyanide anion to replace the diazo group with the cyano group.

Computational modelling of such ion-pair reactions has now become possible,3 and is going to be used here to peek into the future. A B3LYP/6-311G(d,p)/SCRF calculation shows a transition state involving C-N cleavage, with an adjacent cyanide ion doing rather more than merely spectating. The dipole moment of the transition state is 11D (in acetonitrile as solvent). The structure shows the ion-pair endeavouring to minimise the charge separation, with the cyanide approaching at a rather different angle from the departing diazo group. This sort of SN2 displacement at an sp2 (as opposed to sp3) carbon centre is mechanistically quite unusual.4 The free energy of activation for this mechanism is calculated as 24.9 kcal/mol, which is slightly worryingly high for what is considered a room-temperature reaction (the same method gave quite reasonable barriers for another ion-pair mechanism3).

Phenyldiazonium cation + cyanide anion; substitution mechanism. Click for 3D

So time to see if all is what it might seem. There are many other mechanisms that might be explored; below is what seems quite a reasonable one, the elimination of the diazo-group with accompanying proton abstraction to form a benzyne. This transition state has an activation free energy of 17.8 kcal/mol, a much more reasonable value for a room temperature reaction. The dipole moment is 17.1D (the reactant ion-pair is 19.7D).

Benzyne mechanism, in acetonitrile solvent. Click for 3D

So could it be that this veritable reaction actually proceeds via a different mechanism from that in the text books? Benzyne would be formed as a very reactive intermediate, and presumably in the presence of cyanide anions, it would react by nucleophilic addition to form benzonitrile, the same product as before. How could this be verified? Well, if the carbon atom carrying the diazonium group were to be labelled as say 14C, the original mechanism would carry all that label at one carbon in the benzonitrile product. But the benzyne mechanism would scramble the label between two carbons. Janus therefore sees the future in the shape of a useful experiment which could be done to distinguish the two alternative mechanisms.

It is also noteworthy that the two alternative transition states have different dipole moments, and so are affected differently by solvent polarity. Thus in water, the activation free energies are respectively (substitution/elimination) 25.1 and 17.9, whilst in benzene as solvent they are much higher: 48.7 and 39.0 kcal/mol. The effect of the solvent upon the structure of the transition state is also considerable. Below is shown the benzyne elimination mechanism as calculated in the non polar benzene as solvent. Note how the proton transfer is much more advanced, and the C…N cleavage is less advanced than in acetonitrile as solvent.

Benzyne transition state, in benzene solvent. Click for 3D

We are seeing something of a revolution here. Gradually, the mechanisms of the reaction library built up over the last 100 years or so are increasingly being explored using quantitative calculations. It seems entirely likely that more surprises will crop up.

  1. At the age of ~12 I was introduced to chemistry via this reaction, an exposure at least in part why almost 50 years later I am still doing chemistry and why I write this blog.
  2. Kazitsyna, L. A.; Gruzdneva, V. N. Vestnik Moskovskogo Universiteta, Seriya 2: Khimiya, 1975, 16, 331-7.
  3. The ion-pair mechanism of the racemisation of iso-bornyl chloride, another ancient and almost mythological reaction, has recently been studied in this manner; J. Kong, P. v. R. Schleyer and H. S. Rzepa, “Successful Computational Modeling of Iso-bornyl Chloride Ion-Pair Mechanisms”, J. Org. Chem., 2010, DOI: 10.1021/jo100920e
  4. Z. Wu and R. Glaser, “Ab Initio Study of the SN1Ar and SN2Ar Reactions of Benzenediazonium Ion with Water. On the Conception of “Unimolecular Dediazoniation” in Solvolysis Reactions”,  J. Am. Chem. Soc., 2004, DOI: 10.1021/ja047620a



Archived as Henry Rzepa, Janus mechanisms (the past and the future): Reactions of the diazonium cation, URL:http://www.ch.ic.ac.uk/rzepa/blog/?p=3003. Accessed: 2010-12-12. (Archived by WebCite® at http://www.webcitation.org/5uv90cJnU)

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Posted in Interesting chemistry | 3 Comments »

Chemistry with a super-twist: A molecular trefoil knot, part 2.

Tuesday, June 1st, 2010

A conjugated, (apparently) aromatic molecular trefoil might be expected to have some unusual, if not extreme properties. Here some of these are explored.

  1. The first is the vibrational spectrum. With 144 atoms for this molecule, it has 426 vibrational modes, but one is highlighted below. This is the mode that moves the atoms in accord with the Kekulé resonance. If real, this mode resists such alternation. The mode has a value of ~ 1310 cm-1 for benzene, although this is accepted as being lower than expected due to the phenomenon of π-distortivity (DOI: 10.1039/b911817a and also this post). The mode shown below has the value of 1650 cm-1, which is a good deal higher than for benzene. The significant coupling of the CH wagging motions with the C-C/C-N stretching (Duschinsky coupling) makes the interpretation more complex (it also occurs for benzene itself), but the Kekulé mode (there are in fact several) is surprisingly large for so many π-electrons. Perhaps the large degree of writhe noted in the previous post might have something to do with it?

    Molecular trefoil: the Kekulé mode for bond alternation. Click for animation.

  2. The NICS (nucleus independent chemical shift) at the centroid of the trefoil is -16.4 ppm. This is clearly an aromatic value, and confirms our inference that the system is a 4n+2 aromatic molecule. In this example, the aromaticity is not only three-dimensional, but helical as well. The predicted 1H NMR spectrum (below) shows three regions. The upfield region (~ -5 ppm) corresponds to protons pointing directly inwards to the centre, whilst the lowfield region (~ 8ppm) corresponds to protons at the outside edge.

    Predicted 1H NMR spectrum

  3. Shown below is the calculated electronic circular dichroism (ECD) spectrum. It shows a large Cotton effect due to the chiral nature of the trefoil. The electronic transitions extend beyond ~1500nm, approaching the near infra-red. The phase of the Cotton effect at ~600nm calculated for the chiral isomer shown in the 3D model above would certainly suffice to assign the absolute configuration of the system should the experimental spectrum be measurable.

    Calculated Electronic circular dichroism spectrum for the base trefoil.

    The spectrum above shows maximum absorption at ~600nm, which means optical rotation at the sodium D-line (589 nm) cannot be measured (light has to get through to measure its rotation). However, the region of 880nm (the highest value available on commercial spectrometers) is reasonably transparent for such measurement. Calculations may not be much help, since the linear CPHF equations appear unstable. Thus [α]880 shows an enormous dependence on the precise DFT method chosen to compute it (~ +8763°@CAM-B3LYP but the very different -59898°@B3LYP).

Henry Rzepa. Chemistry with a super-twist: A molecular trefoil knot, part 2.. . 2010-06-02. URL:http://www.ch.ic.ac.uk/rzepa/blog/?p=2084. Accessed: 2010-06-02. (Archived by WebCite® at http://www.webcitation.org/5qC4NiFsM)

 

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