Posts Tagged ‘higher energy’

« Older Entries

Imaging normal vibrational modes of a single molecule of CoTPP: a mystery about the nature of the imaged species.

Thursday, April 25th, 2019

Previously, I explored (computationally) the normal vibrational modes of Co(II)-tetraphenylporphyrin (CoTPP) as a “flattened” species on copper or gold surfaces for comparison with those recently imaged[1]. The initial intent was to estimate the “flattening” energy. There are six electronic possibilities for this molecule on a metal surface. Respectively positively, or negatively charged and a neutral species, each in either a low or a high-spin electronic state. I reported five of these earlier, finding each had quite high barriers for “flattening” the molecule. For the final 6th possibility, the triplet anion, the SCF (self-consistent-field) had failed to converge, but for which I can now report converged results.†

charge

Spin

Multiplicity

 ΔG, Twisted Ph,
Hartree		 ΔG, “flattened”,
Hartree

ΔΔG,

kcal/mol
-1 Triplet -3294.68134 (C2) -3294.64735 (C2v) 21.3
-3294.60006 (Cs) 51.0
-3294.37012 (D2h) 195.3
Singlet -3294.67713 (S4) -3294.39418 (D4h) 175.6
-3294.39321 (D2h) 178.2
-3294.56652 (D2) 69.4
FAIR data at DOI: 10.14469/hpc/5486

I am exploring the so-called “flattened” mode, induced by the voltage applied at the tip of the STM (scanning-tunnelling microscope) probe and which causes the phenyl rings to rotate as per above. This rotation in turn causes the hydrogen atom-pair encircled above to approach each other very closely.‡ To avoid these repulsions, the molecule buckles into one of two modes. The first causes the phenyl rings to stack up/down/up/down. The second involves an all-up stacking, as shown below. Although these are in fact 4th-order saddle points as isolated molecules, the STM voltage can inject sufficient energy to convert these into apparently stable minima on the metal surface.

All syn mode, Triplet anion

The up/down/up/down “flattened” form (below) shows a much more modest planarisation energy than all the other charged/neutral states reported in the previous post, whereas the all-up isomer (which on the face of it looks a far easier proposition to come into close contact with a metal surface) is far higher in free energy.

The caption to Figure 3 in the original article[1] does not explicitly mention the nature of the metal surface on which the vibrations were recorded, but we do get “The intensity in the upper right corner of the 320-cm−1 map is from a neighbouring Cu–CO stretch” which suggests it is in fact a copper surface. Coupled with the other observation that in “contrast to gold, the Kondo resonance of cobalt disappears on Cu(100), suggesting that it acquires nearly a full electron from the metal (see Extended Data Fig. 2),” the model below of a triplet-state anion on the Cu surface seems the most appropriate.

Syn/anti mode, Triplet anion with C2v symmetry

There is one final remark made in the article worth repeating here: “This suggests that the vibronic functions are complex-valued in this state, as expected for Jahn–Teller active degenerate orbitals of the planar porphyrin.26” Orbital degeneracy can only occur if the molecule has e.g. D4h point group symmetry, whereas the triplet anion stationary-point shown in the figure above has only C2v symmetry for which no orbital degeneracies (E) are expected. Enforcing D4h symmetry on Co(II) tetraphenylporphyrin results in eight pairs of H…H contacts of 1.34Å,‡ which is an impossibly short distance (the shortest known is ~1.5Å). Moreover this geometry has an equally impossible free energy 176 kcal/mol above the relaxed free molecule. Visually from Figure 3, the H…H contact distance looks even shorter (below, circled in red)! A D2h form (with no E-type orbitals) can also be located.

Singlet, Calculated with D4h symmetry. Click for vibrations.

Singlet, Calculated with D2h symmetry. Click for vibrations.

Taken from Figure 3 (Ref 1).

These totally flat species are calculated to be at 13 or 12th-order saddle points, with the eight most negative force constants having vectors which correspond to up/down avoidance motions of the proximate hydrogen pairs encircled above and the remaining being buckling modes of the entire ring.

So to the mystery, being the nature of the “flattened” CoTPP on the copper metal surface, as represented in Figure 3 of the article.[1] Is it truly flat, as implied by the article? If so, the energy of such a species would be beyond the limits of what is normally considered feasible. Moreover, it would represent a species with truly mind-blowing short H…H contacts. Or could it be a saddle-shaped geometry, where the phenyl rings are not lying flat in contact with the metal but interacting via the phenyl para-hydrogens? That geometry has not only a much more reasonable energy above the unflattened free molecule, but also acceptable H…H contacts (~2.0.Å) However, would such a shape correspond to the visualised vibrational modes also shown in Figure 3? I have a feeling that there must be more to this story.

†These convergence problems were solved by improving the basis set via adding “diffuse” functions, as in (u)ωB97XD/6-311+G(d,p). ‡If the crystal structure for these species is flattened without geometry optimisation, the H-H distance is around 0.8Å

References

  1. J. Lee, K.T. Crampton, N. Tallarida, and V.A. Apkarian, "Visualizing vibrational normal modes of a single molecule with atomically confined light", Nature, vol. 568, pp. 78-82, 2019. https://doi.org/10.1038/s41586-019-1059-9

Tags:, , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , ,
Posted in Interesting chemistry | 1 Comment »

Ritonavir: a look at a famous example of conformational polymorphism.

Monday, January 2nd, 2017

Here is an inside peek at another one of Derek Lowe’s 250 milestones in chemistry, the polymorphism of Ritonavir.[1] The story in a nutshell concerns one of a pharma company’s worst nightmares; a drug which has been successfully brought to market unexpectedly “changes” after a few years on market to a less effective form (or to use the drug term, formulation). This can happen via a phenomenon known as polymorphism, where the crystalline structure of a molecule can have more than one form. In this case, form I was formulated into soluble tablets for oral intake. During later manufacturing, a new less-soluble form appeared and “within weeks this new polymorph began to appear throughout both the bulk drug and formulation areas“[1]

The structure of the original form I is shown below (3D DOI: 10.5517/CCRVC75). The compound has three HN-CO peptide linkages, all of which are in the stereoelectronically favoured s-cis form, with a dihedral angle of 180° across the H-N and C=O vectors.

Click for 3D

To show how favourable this s-cis form is, here is a search of the Cambridge structural database for acyclic HN-C=O bonds; of the ~8200 examples, only 5 have an s-trans torsion of ~180°. It is I feel statistically not entirely correct to convert this ratio of K=1640 to a free energy, but if one does, then at 298K, RTlnK works out to 4.4 kcal/mol. Note also that two compounds show an angle of ~90° (artefacts?).

The new type-II form that emerged has only two s-cis peptide linkages, and the third has isomerised to this higher energy s-trans form (3D DOI: 10.5517/CCRVC97)

Click for 3D

This has various knock-on effects on the conformation of the actual molecule itself.

  1. The cis-trans isomerisation of a peptide or amide bond is a relatively high energy process, since the C=N bond order is higher than 1. For example, in the 1H NMR spectrum of N,N-dimethyl formamide at room temperature, one can famously observe two methyl resonances and it is only at higher temperatures that the two signals coalesce due to more rapid rotation about the C=N bond.
  2. A pedant might query whether this isomerism is correctly termed a conformational or a configurational change? High-energy rotations that result in cis/trans isomerisms are normally referred to as a configurational changes, whereas low energy rotations about e.g. single bonds are known as conformational changes (thus the conformational changes in cyclohexane). There is a grey region such as this one, where the boundary between the two terms is encountered. 
  3. This isomerism has the knock-on effect of inducing a much lower energy rotation of a C-C single bond (on the left hand side of the representations above), rotating from a dihedral angle of +193 in form I to +51 in form II.
  4. More minor affects are seen in the conformation of the central benzyl group and the S/N heterocyclic ring on the right hand side.
  5. All these low energy conformational effects occur because a better hydrogen bonding network can then be set up in the crystal lattice, something not easily predictable  from the diagrams of the single molecules shown above.
  6. Overall, the free energy of the lattice is lower, despite the higher energy of the s-trans peptide bond. 
  7. Clearly, the dynamics of crystallisation initially favoured form I (despite the higher energy of the crystallised outcome), but if a tiny seed of form II is present (or perhaps other impurities) this can dramatically (but unpredictably) change these crystallisation dynamics.

I suspect that since 1998 when this story unfolded, all new drugs in which one or more s-cis peptide bonds are present have caused anxiety. In the system above for example, one might ask whether cis/trans isomerisation of instead either of the other two peptide bonds present might have similar results? Or hypothesize whether inhibiting the associated rotation of the C-C single bond noted above by appropriate “tethering” might prevent form I from converting to form II. Since 1998, I am sure trying to predict the solid form of an organic molecule from its isolated structure using computational methods has dramatically increased, although I have not found in SciFinder any reported instances of such modelling for Ritonavir itself.[2] Perhaps, if such a method were found, it might be too commercially valuable to share?

References

  1. J. Bauer, S. Spanton, R. Henry, J. Quick, W. Dziki, W. Porter, and J. Morris, "Ritonavir: An Extraordinary Example of Conformational Polymorphism", Pharmaceutical Research, vol. 18, pp. 859-866, 2001. https://doi.org/10.1023/a:1011052932607
  2. S.R. Chemburkar, J. Bauer, K. Deming, H. Spiwek, K. Patel, J. Morris, R. Henry, S. Spanton, W. Dziki, W. Porter, J. Quick, P. Bauer, J. Donaubauer, B.A. Narayanan, M. Soldani, D. Riley, and K. McFarland, "Dealing with the Impact of Ritonavir Polymorphs on the Late Stages of Bulk Drug Process Development", Organic Process Research & Development, vol. 4, pp. 413-417, 2000. https://doi.org/10.1021/op000023y

Tags:, , , , , , , , , , , , , , , , , , , , , ,
Posted in Interesting chemistry | No Comments »

An unusual [1,6] shift in homotropylium cation exhibiting zones of aromaticity.

Tuesday, August 12th, 2014

One thing leads to another. Thus in the previous post, I described a thermal pericyclic reaction that appears to exhibit two transition states resulting in two different stereochemical outcomes. I noted that another such reaction appeared to be a [1,6] carousel migration in homotropylium cation,[1] where transition states for both retention and inversion of the configuration of the migrating group (respectively formally allowed and forbidden) were reported (scheme below). Here I explore this system further. homotropylium Firstly, the pathway leading to inversion.[2] The reaction path (ωB97XD/6-311G(d,p)/SCRF=chloroform) has got a very odd (table-top mountain) shape, whereby the region of the transition state (IRC = 0.0) is very flat, and the region close to reactant and (identical) product is very steep. The gradient norm shows this best, with sharp spikes at IRC ± 4.2. Something clearly is happening here to cause this behaviour. Before moving on to analyze this, I want you first to observe the methyl groups below. Note how one of them rotates at the start of the process, and the other at the end. I have elsewhere called this behaviour the methyl flag, and it is due to stereoelectronic re-alignments of the C-H groups accompanying the changes in the conjugated array. htropa htrop htropG The homotropylium cation is said to be homoaromatic, indicating that cyclic conjugation can be maintained across a ring in which the σ framework is interrupted at one point. A NICS probe placed at the ring critical point of this molecule reveals a chemical shift of -11.3 ppm[3], very similar to eg that obtained for benzene itself. The three highest doubly occupied NBOs (below) show two normal π-type orbitals and one rather different one that spans the homo-bond (the MOs, before you ask, are a bit of a mess, with lots of mixed contributions from other parts of the σ framework).

HONBO (two) HONBO-2

Click for 3D

Click for 3D

Click for 3D

Click for 3D

At the transition state for the [1,6] migration, the same NICS probe registers a value of +2.6 ppm[4], now firmly in the non-aromatic zone. So this reaction is characterised by two zones, ring-aromatic ones at the start and the end of the process, and a higher energy non-aromatic one in the middle of the reaction pathway as ~enclosed by the region of IRC ± 4.2. The homo-bond in the aromatic zone starts with a length of 1.74Å, reduces to 1.53Å at the transition state and ends up as a normal aromatic bond of length 1.41Å. Meanwhile, the relocated homo-bond changes in the opposite sense, starting as a normal aromatic length of 1.41Å, becoming 1.53Å at the transition state and ending as a homo-length of 1.74Å. Presumably, virtually full strength homoaromaticity can be sustained for a homo-bond of 1.74Å, but as that bond mutates to a σ-bond of 1.53Å, the cyclic conjugation falls off the edge of the cliff, to be restored only at the end. Pericyclic reactions are themselves said to sustain aromatic transition states,[5] and so a simplistic way of looking at this is that the “aromaticity” relocates (or morphs) from the reactant to the transition state, and then back again during the course of the migration. A reaction path from which one can indeed learn a lot.

Now to the pathway in which the migrating group retains configuration. This is no longer a single step concerted reaction,[6] since at the half-way point we no longer have a transition state but a shallow intermediate (~IRC +2, [7]). It (formally at least) becomes a two-step non-concerted process, and the overall barrier is ~5 kcal/mol lower than for the inversion path. The aromaticity changes in a similar manner to before (i.e. IRC ~-5).htrop-ra

Htrop-retHtrop-retG

So this emerges as not quite the example I thought it was, but nonetheless unusual with the “forbidden” pathway being concerted and the “allowed” pathway being non-concerted. Molecular dynamics on these two systems would indeed be interesting to see what proportion of the trajectories go via each pathway.

References

  1. A.M. Genaev, G.E. Sal’nikov, and V.G. Shubin, "Energy barriers to carousel rearrangements of carbocations: Quantum-chemical calculations vs. experiment", Russian Journal of Organic Chemistry, vol. 43, pp. 1134-1138, 2007. https://doi.org/10.1134/s1070428007080076
  2. H.S. Rzepa, "Gaussian Job Archive for C10H13(1+)", 2014. https://doi.org/10.6084/m9.figshare.1134556
  3. H.S. Rzepa, "Gaussian Job Archive for C10H13(1+)", 2014. https://doi.org/10.6084/m9.figshare.1135694
  4. H.S. Rzepa, "Gaussian Job Archive for C10H13(1+)", 2014. https://doi.org/10.6084/m9.figshare.1135695
  5. H.S. Rzepa, "The Aromaticity of Pericyclic Reaction Transition States", Journal of Chemical Education, vol. 84, pp. 1535, 2007. https://doi.org/10.1021/ed084p1535
  6. H.S. Rzepa, "Gaussian Job Archive for C10H13(1+)", 2014. https://doi.org/10.6084/m9.figshare.1135668
  7. H.S. Rzepa, "Gaussian Job Archive for C10H13(1+)", 2014. https://doi.org/10.6084/m9.figshare.1134559

Tags:, ,
Posted in pericyclic, reaction mechanism | 5 Comments »

A connected world (journals and blogs): The benzene dication.

Thursday, April 10th, 2014

Science is rarely about a totally new observation or rationalisation, it is much more about making connections between known facts, and perhaps using these connections to extrapolate to new areas (building on the shoulders of giants, etc). So here I chart one example of such connectivity over a period of six years.

The story starts with this article[1], a preview talk about which (Hypervalent Carbon Atom: “Freezing” the SN2 Transition State) I actually saw at an ACS conference a year or so earlier. When the article was published, Steve Bachrach blogged about it, noting the claim for pentavalent carbon. The semantics of a valency vs a coordination are subtle, and I was not convinced that this frozen transition state deserved its elevation from penta-coordinate to pentavalent. After some discussion on Steve’s blog, I built upon these ideas with a few thoughts of my own on the present blog and then wondered whether they could be finally distilled into a more formal publication (testing the precedent in some ways of whether collaborative and public discussions of ideas could be published formally, or whether they would be rejected as having been already “published”). Well, these final distilled thoughts were indeed published in 2010[2], including their genesis in Steve’s blog (I wanted to put blogs more firmly into the acceptable scientific circle). This article included one species (numbered 5 in that article in 2010[2]) and pointed out an analogy to replacing CH2+ by e.g the isoelectronic BH1+, in as much as an example of the latter is indeed known as a stable crystalline compound.[3]. Iso-electronics is a very fruitful source of connections in chemistry!

5

Matters rested there until yesterday, when I spotted this on Steve’s blog where he discusses this recent article on the structure of the benzene dication.[4] Hey presto, there is that molecule again, but now there is firm experimental evidence of its existence! It was I think rather too much to expect the authors of this article to have spotted the connection to mine (although as it happens, both address the issue of complexes to He). The relationship between CH2+ and BH1+ is a little more subtle. From my point of view, it is always worth trawling through the crystal structure database in favour of evidence for hypothetical species (or their isoelectronic substitutions), and so it proved in this case!

There are other connections possible. Thus the dication of benzene has a (higher energy) isomer which is in fact a 4π antiaromatic species which avoids this antiaromaticity by a geometric distortion, with two C-H bonds bending above and below the ring. Such avoided antiaromaticity has been noted elsewhere here.

There is one final connection for me to make. My 2010 article[2] contained one of my interactive tables containing the data for the various structures (yes, although its data, you will need to have a subscription to the journal to access it). As it happens, last year we wished to reprise this style of publication, but as I blogged at the time, the journal had changed its production processes, and they could no longer offer me that opportunity. Some quick thinking came up with a replacement, which we now use extensively.[5] So the chain of connections resulting from that original talk some six years ago continues.

<

p>As for that chain, it arose distressingly randomly. I do not routinely read the entire ToC of JACS and so would not have discovered[4] the connection by that route. Fortunately, Steve Bachrach does and helped me make that connection to the molecule shown above. Although I did spend a few minutes thinking to myself “does that structure ring any bells?”. Fortunately, one did (eventually) ring. But for every connection made in this wonderfully human manner, I cannot help but think how many are not! However, if connections were much easier to make, could we as humans cope with the overwhelming deluge of new ideas?

References

  1. S. Pierrefixe, S. van Stralen, J. van Stralen, C. Fonseca Guerra, and F. Bickelhaupt, "Hypervalent Carbon Atom: “Freezing” the S<sub>N</sub>2 Transition State", Angewandte Chemie International Edition, vol. 48, pp. 6469-6471, 2009. https://doi.org/10.1002/anie.200902125
  2. H.S. Rzepa, "The rational design of helium bonds", Nature Chemistry, vol. 2, pp. 390-393, 2010. https://doi.org/10.1038/nchem.596
  3. C. Dohmeier, R. Köppe, C. Robl, and H. Schnöckel, "Kristallstruktur von [Cp★BBr][AlBr4]", Journal of Organometallic Chemistry, vol. 487, pp. 127-130, 1995. https://doi.org/10.1016/0022-328x(94)05089-t
  4. J. Jašík, D. Gerlich, and J. Roithová, "Probing Isomers of the Benzene Dication in a Low-Temperature Trap", Journal of the American Chemical Society, vol. 136, pp. 2960-2962, 2014. https://doi.org/10.1021/ja412109h
  5. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-García, M.J. Harvey, N.J. Mason, and H.S. Rzepa, "The Houk–List transition states for organocatalytic mechanisms revisited", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b

Tags:, , ,
Posted in Hypervalency, Interesting chemistry | No Comments »

A connected world (journals and blogs): The benzene dication.

Thursday, April 10th, 2014

Science is rarely about a totally new observation or rationalisation, it is much more about making connections between known facts, and perhaps using these connections to extrapolate to new areas (building on the shoulders of giants, etc). So here I chart one example of such connectivity over a period of six years.

The story starts with this article[1], a preview talk about which (Hypervalent Carbon Atom: “Freezing” the SN2 Transition State) I actually saw at an ACS conference a year or so earlier. When the article was published, Steve Bachrach blogged about it, noting the claim for pentavalent carbon. The semantics of a valency vs a coordination are subtle, and I was not convinced that this frozen transition state deserved its elevation from penta-coordinate to pentavalent. After some discussion on Steve’s blog, I built upon these ideas with a few thoughts of my own on the present blog and then wondered whether they could be finally distilled into a more formal publication (testing the precedent in some ways of whether collaborative and public discussions of ideas could be published formally, or whether they would be rejected as having been already “published”). Well, these final distilled thoughts were indeed published in 2010[2], including their genesis in Steve’s blog (I wanted to put blogs more firmly into the acceptable scientific circle). This article included one species (numbered 5 in that article in 2010[2]) and pointed out an analogy to replacing CH2+ by e.g the isoelectronic BH1+, in as much as an example of the latter is indeed known as a stable crystalline compound.[3]. Iso-electronics is a very fruitful source of connections in chemistry!

5

Matters rested there until yesterday, when I spotted this on Steve’s blog where he discusses this recent article on the structure of the benzene dication.[4] Hey presto, there is that molecule again, but now there is firm experimental evidence of its existence! It was I think rather too much to expect the authors of this article to have spotted the connection to mine (although as it happens, both address the issue of complexes to He). The relationship between CH2+ and BH1+ is a little more subtle. From my point of view, it is always worth trawling through the crystal structure database in favour of evidence for hypothetical species (or their isoelectronic substitutions), and so it proved in this case!

There are other connections possible. Thus the dication of benzene has a (higher energy) isomer which is in fact a 4π antiaromatic species which avoids this antiaromaticity by a geometric distortion, with two C-H bonds bending above and below the ring. Such avoided antiaromaticity has been noted elsewhere here.

There is one final connection for me to make. My 2010 article[2] contained one of my interactive tables containing the data for the various structures (yes, although its data, you will need to have a subscription to the journal to access it). As it happens, last year we wished to reprise this style of publication, but as I blogged at the time, the journal had changed its production processes, and they could no longer offer me that opportunity. Some quick thinking came up with a replacement, which we now use extensively.[5] So the chain of connections resulting from that original talk some six years ago continues.

<

p>As for that chain, it arose distressingly randomly. I do not routinely read the entire ToC of JACS and so would not have discovered[4] the connection by that route. Fortunately, Steve Bachrach does and helped me make that connection to the molecule shown above. Although I did spend a few minutes thinking to myself “does that structure ring any bells?”. Fortunately, one did (eventually) ring. But for every connection made in this wonderfully human manner, I cannot help but think how many are not! However, if connections were much easier to make, could we as humans cope with the overwhelming deluge of new ideas?

References

  1. S. Pierrefixe, S. van Stralen, J. van Stralen, C. Fonseca Guerra, and F. Bickelhaupt, "Hypervalent Carbon Atom: “Freezing” the S<sub>N</sub>2 Transition State", Angewandte Chemie International Edition, vol. 48, pp. 6469-6471, 2009. https://doi.org/10.1002/anie.200902125
  2. H.S. Rzepa, "The rational design of helium bonds", Nature Chemistry, vol. 2, pp. 390-393, 2010. https://doi.org/10.1038/nchem.596
  3. C. Dohmeier, R. Köppe, C. Robl, and H. Schnöckel, "Kristallstruktur von [Cp★BBr][AlBr4]", Journal of Organometallic Chemistry, vol. 487, pp. 127-130, 1995. https://doi.org/10.1016/0022-328x(94)05089-t
  4. J. Jašík, D. Gerlich, and J. Roithová, "Probing Isomers of the Benzene Dication in a Low-Temperature Trap", Journal of the American Chemical Society, vol. 136, pp. 2960-2962, 2014. https://doi.org/10.1021/ja412109h
  5. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-García, M.J. Harvey, N.J. Mason, and H.S. Rzepa, "The Houk–List transition states for organocatalytic mechanisms revisited", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b

Tags:, , ,
Posted in Hypervalency, Interesting chemistry | No Comments »

A connected world (journals and blogs): The benzene dication.

Thursday, April 10th, 2014

Science is rarely about a totally new observation or rationalisation, it is much more about making connections between known facts, and perhaps using these connections to extrapolate to new areas (building on the shoulders of giants, etc). So here I chart one example of such connectivity over a period of six years.

The story starts with this article[1], a preview talk about which (Hypervalent Carbon Atom: “Freezing” the SN2 Transition State) I actually saw at an ACS conference a year or so earlier. When the article was published, Steve Bachrach blogged about it, noting the claim for pentavalent carbon. The semantics of a valency vs a coordination are subtle, and I was not convinced that this frozen transition state deserved its elevation from penta-coordinate to pentavalent. After some discussion on Steve’s blog, I built upon these ideas with a few thoughts of my own on the present blog and then wondered whether they could be finally distilled into a more formal publication (testing the precedent in some ways of whether collaborative and public discussions of ideas could be published formally, or whether they would be rejected as having been already “published”). Well, these final distilled thoughts were indeed published in 2010[2], including their genesis in Steve’s blog (I wanted to put blogs more firmly into the acceptable scientific circle). This article included one species (numbered 5 in that article in 2010[2]) and pointed out an analogy to replacing CH2+ by e.g the isoelectronic BH1+, in as much as an example of the latter is indeed known as a stable crystalline compound.[3]. Iso-electronics is a very fruitful source of connections in chemistry!

5

Matters rested there until yesterday, when I spotted this on Steve’s blog where he discusses this recent article on the structure of the benzene dication.[4] Hey presto, there is that molecule again, but now there is firm experimental evidence of its existence! It was I think rather too much to expect the authors of this article to have spotted the connection to mine (although as it happens, both address the issue of complexes to He). The relationship between CH2+ and BH1+ is a little more subtle. From my point of view, it is always worth trawling through the crystal structure database in favour of evidence for hypothetical species (or their isoelectronic substitutions), and so it proved in this case!

There are other connections possible. Thus the dication of benzene has a (higher energy) isomer which is in fact a 4π antiaromatic species which avoids this antiaromaticity by a geometric distortion, with two C-H bonds bending above and below the ring. Such avoided antiaromaticity has been noted elsewhere here.

There is one final connection for me to make. My 2010 article[2] contained one of my interactive tables containing the data for the various structures (yes, although its data, you will need to have a subscription to the journal to access it). As it happens, last year we wished to reprise this style of publication, but as I blogged at the time, the journal had changed its production processes, and they could no longer offer me that opportunity. Some quick thinking came up with a replacement, which we now use extensively.[5] So the chain of connections resulting from that original talk some six years ago continues.

<

p>As for that chain, it arose distressingly randomly. I do not routinely read the entire ToC of JACS and so would not have discovered[4] the connection by that route. Fortunately, Steve Bachrach does and helped me make that connection to the molecule shown above. Although I did spend a few minutes thinking to myself “does that structure ring any bells?”. Fortunately, one did (eventually) ring. But for every connection made in this wonderfully human manner, I cannot help but think how many are not! However, if connections were much easier to make, could we as humans cope with the overwhelming deluge of new ideas?

References

  1. S. Pierrefixe, S. van Stralen, J. van Stralen, C. Fonseca Guerra, and F. Bickelhaupt, "Hypervalent Carbon Atom: “Freezing” the S<sub>N</sub>2 Transition State", Angewandte Chemie International Edition, vol. 48, pp. 6469-6471, 2009. https://doi.org/10.1002/anie.200902125
  2. H.S. Rzepa, "The rational design of helium bonds", Nature Chemistry, vol. 2, pp. 390-393, 2010. https://doi.org/10.1038/nchem.596
  3. C. Dohmeier, R. Köppe, C. Robl, and H. Schnöckel, "Kristallstruktur von [Cp★BBr][AlBr4]", Journal of Organometallic Chemistry, vol. 487, pp. 127-130, 1995. https://doi.org/10.1016/0022-328x(94)05089-t
  4. J. Jašík, D. Gerlich, and J. Roithová, "Probing Isomers of the Benzene Dication in a Low-Temperature Trap", Journal of the American Chemical Society, vol. 136, pp. 2960-2962, 2014. https://doi.org/10.1021/ja412109h
  5. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-García, M.J. Harvey, N.J. Mason, and H.S. Rzepa, "The Houk–List transition states for organocatalytic mechanisms revisited", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b

Tags:, , ,
Posted in Hypervalency, Interesting chemistry | No Comments »

A connected world (journals and blogs): The benzene dication.

Thursday, April 10th, 2014

Science is rarely about a totally new observation or rationalisation, it is much more about making connections between known facts, and perhaps using these connections to extrapolate to new areas (building on the shoulders of giants, etc). So here I chart one example of such connectivity over a period of six years.

The story starts with this article[1], a preview talk about which (Hypervalent Carbon Atom: “Freezing” the SN2 Transition State) I actually saw at an ACS conference a year or so earlier. When the article was published, Steve Bachrach blogged about it, noting the claim for pentavalent carbon. The semantics of a valency vs a coordination are subtle, and I was not convinced that this frozen transition state deserved its elevation from penta-coordinate to pentavalent. After some discussion on Steve’s blog, I built upon these ideas with a few thoughts of my own on the present blog and then wondered whether they could be finally distilled into a more formal publication (testing the precedent in some ways of whether collaborative and public discussions of ideas could be published formally, or whether they would be rejected as having been already “published”). Well, these final distilled thoughts were indeed published in 2010[2], including their genesis in Steve’s blog (I wanted to put blogs more firmly into the acceptable scientific circle). This article included one species (numbered 5 in that article in 2010[2]) and pointed out an analogy to replacing CH2+ by e.g the isoelectronic BH1+, in as much as an example of the latter is indeed known as a stable crystalline compound.[3]. Iso-electronics is a very fruitful source of connections in chemistry!

5

Matters rested there until yesterday, when I spotted this on Steve’s blog where he discusses this recent article on the structure of the benzene dication.[4] Hey presto, there is that molecule again, but now there is firm experimental evidence of its existence! It was I think rather too much to expect the authors of this article to have spotted the connection to mine (although as it happens, both address the issue of complexes to He). The relationship between CH2+ and BH1+ is a little more subtle. From my point of view, it is always worth trawling through the crystal structure database in favour of evidence for hypothetical species (or their isoelectronic substitutions), and so it proved in this case!

There are other connections possible. Thus the dication of benzene has a (higher energy) isomer which is in fact a 4π antiaromatic species which avoids this antiaromaticity by a geometric distortion, with two C-H bonds bending above and below the ring. Such avoided antiaromaticity has been noted elsewhere here.

There is one final connection for me to make. My 2010 article[2] contained one of my interactive tables containing the data for the various structures (yes, although its data, you will need to have a subscription to the journal to access it). As it happens, last year we wished to reprise this style of publication, but as I blogged at the time, the journal had changed its production processes, and they could no longer offer me that opportunity. Some quick thinking came up with a replacement, which we now use extensively.[5] So the chain of connections resulting from that original talk some six years ago continues.

<

p>As for that chain, it arose distressingly randomly. I do not routinely read the entire ToC of JACS and so would not have discovered[4] the connection by that route. Fortunately, Steve Bachrach does and helped me make that connection to the molecule shown above. Although I did spend a few minutes thinking to myself “does that structure ring any bells?”. Fortunately, one did (eventually) ring. But for every connection made in this wonderfully human manner, I cannot help but think how many are not! However, if connections were much easier to make, could we as humans cope with the overwhelming deluge of new ideas?

References

  1. S. Pierrefixe, S. van Stralen, J. van Stralen, C. Fonseca Guerra, and F. Bickelhaupt, "Hypervalent Carbon Atom: “Freezing” the S<sub>N</sub>2 Transition State", Angewandte Chemie International Edition, vol. 48, pp. 6469-6471, 2009. https://doi.org/10.1002/anie.200902125
  2. H.S. Rzepa, "The rational design of helium bonds", Nature Chemistry, vol. 2, pp. 390-393, 2010. https://doi.org/10.1038/nchem.596
  3. C. Dohmeier, R. Köppe, C. Robl, and H. Schnöckel, "Kristallstruktur von [Cp★BBr][AlBr4]", Journal of Organometallic Chemistry, vol. 487, pp. 127-130, 1995. https://doi.org/10.1016/0022-328x(94)05089-t
  4. J. Jašík, D. Gerlich, and J. Roithová, "Probing Isomers of the Benzene Dication in a Low-Temperature Trap", Journal of the American Chemical Society, vol. 136, pp. 2960-2962, 2014. https://doi.org/10.1021/ja412109h
  5. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-García, M.J. Harvey, N.J. Mason, and H.S. Rzepa, "The Houk–List transition states for organocatalytic mechanisms revisited", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b

Tags:, , ,
Posted in Hypervalency, Interesting chemistry | No Comments »

A connected world (journals and blogs): The benzene dication.

Thursday, April 10th, 2014

Science is rarely about a totally new observation or rationalisation, it is much more about making connections between known facts, and perhaps using these connections to extrapolate to new areas (building on the shoulders of giants, etc). So here I chart one example of such connectivity over a period of six years.
The story starts with this article[1], a preview talk about which (Hypervalent Carbon Atom: “Freezing” the SN2 Transition State) I actually saw at an ACS conference a year or so earlier. When the article was published, Steve Bachrach blogged about it, noting the claim for pentavalent carbon. The semantics of a valency vs a coordination are subtle, and I was not convinced that this frozen transition state deserved its elevation from penta-coordinate to pentavalent. After some discussion on Steve’s blog, I built upon these ideas with a few thoughts of my own on the present blog and then wondered whether they could be finally distilled into a more formal publication (testing the precedent in some ways of whether collaborative and public discussions of ideas could be published formally, or whether they would be rejected as having been already “published”). Well, these final distilled thoughts were indeed published in 2010[2], including their genesis in Steve’s blog (I wanted to put blogs more firmly into the acceptable scientific circle). This article included one species (numbered 5 in that article in 2010[2]) and pointed out an analogy to replacing CH2+ by e.g the isoelectronic BH1+, in as much as an example of the latter is indeed known as a stable crystalline compound.[3]. Iso-electronics is a very fruitful source of connections in chemistry!
5
Matters rested there until yesterday, when I spotted this on Steve’s blog where he discusses this recent article on the structure of the benzene dication.[4] Hey presto, there is that molecule again, but now there is firm experimental evidence of its existence! It was I think rather too much to expect the authors of this article to have spotted the connection to mine (although as it happens, both address the issue of complexes to He). The relationship between CH2+ and BH1+ is a little more subtle. From my point of view, it is always worth trawling through the crystal structure database in favour of evidence for hypothetical species (or their isoelectronic substitutions), and so it proved in this case!
There are other connections possible. Thus the dication of benzene has a (higher energy) isomer which is in fact a 4π antiaromatic species which avoids this antiaromaticity by a geometric distortion, with two C-H bonds bending above and below the ring. Such avoided antiaromaticity has been noted elsewhere here.
There is one final connection for me to make. My 2010 article[2] contained one of my interactive tables containing the data for the various structures (yes, although its data, you will need to have a subscription to the journal to access it). As it happens, last year we wished to reprise this style of publication, but as I blogged at the time, the journal had changed its production processes, and they could no longer offer me that opportunity. Some quick thinking came up with a replacement, which we now use extensively.[5] So the chain of connections resulting from that original talk some six years ago continues.
<
p>As for that chain, it arose distressingly randomly. I do not routinely read the entire ToC of JACS and so would not have discovered[4] the connection by that route. Fortunately, Steve Bachrach does and helped me make that connection to the molecule shown above. Although I did spend a few minutes thinking to myself “does that structure ring any bells?”. Fortunately, one did (eventually) ring. But for every connection made in this wonderfully human manner, I cannot help but think how many are not! However, if connections were much easier to make, could we as humans cope with the overwhelming deluge of new ideas?

References

  1. S. Pierrefixe, S. van Stralen, J. van Stralen, C. Fonseca Guerra, and F. Bickelhaupt, "Hypervalent Carbon Atom: “Freezing” the S<sub>N</sub>2 Transition State", Angewandte Chemie International Edition, vol. 48, pp. 6469-6471, 2009. https://doi.org/10.1002/anie.200902125
  2. H.S. Rzepa, "The rational design of helium bonds", Nature Chemistry, vol. 2, pp. 390-393, 2010. https://doi.org/10.1038/nchem.596
  3. C. Dohmeier, R. Köppe, C. Robl, and H. Schnöckel, "Kristallstruktur von [Cp★BBr][AlBr4]", Journal of Organometallic Chemistry, vol. 487, pp. 127-130, 1995. https://doi.org/10.1016/0022-328x(94)05089-t
  4. J. Jašík, D. Gerlich, and J. Roithová, "Probing Isomers of the Benzene Dication in a Low-Temperature Trap", Journal of the American Chemical Society, vol. 136, pp. 2960-2962, 2014. https://doi.org/10.1021/ja412109h
  5. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-García, M.J. Harvey, N.J. Mason, and H.S. Rzepa, "The Houk–List transition states for organocatalytic mechanisms revisited", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b

Tags:, , ,
Posted in Hypervalency, Interesting chemistry | No Comments »

A connected world (journals and blogs): The benzene dication.

Thursday, April 10th, 2014

Science is rarely about a totally new observation or rationalisation, it is much more about making connections between known facts, and perhaps using these connections to extrapolate to new areas (building on the shoulders of giants, etc). So here I chart one example of such connectivity over a period of six years.

The story starts with this article[1], a preview talk about which (Hypervalent Carbon Atom: “Freezing” the SN2 Transition State) I actually saw at an ACS conference a year or so earlier. When the article was published, Steve Bachrach blogged about it, noting the claim for pentavalent carbon. The semantics of a valency vs a coordination are subtle, and I was not convinced that this frozen transition state deserved its elevation from penta-coordinate to pentavalent. After some discussion on Steve’s blog, I built upon these ideas with a few thoughts of my own on the present blog and then wondered whether they could be finally distilled into a more formal publication (testing the precedent in some ways of whether collaborative and public discussions of ideas could be published formally, or whether they would be rejected as having been already “published”). Well, these final distilled thoughts were indeed published in 2010[2], including their genesis in Steve’s blog (I wanted to put blogs more firmly into the acceptable scientific circle). This article included one species (numbered 5 in that article in 2010[2]) and pointed out an analogy to replacing CH2+ by e.g the isoelectronic BH1+, in as much as an example of the latter is indeed known as a stable crystalline compound.[3]. Iso-electronics is a very fruitful source of connections in chemistry!

5

Matters rested there until yesterday, when I spotted this on Steve’s blog where he discusses this recent article on the structure of the benzene dication.[4] Hey presto, there is that molecule again, but now there is firm experimental evidence of its existence! It was I think rather too much to expect the authors of this article to have spotted the connection to mine (although as it happens, both address the issue of complexes to He). The relationship between CH2+ and BH1+ is a little more subtle. From my point of view, it is always worth trawling through the crystal structure database in favour of evidence for hypothetical species (or their isoelectronic substitutions), and so it proved in this case!

There are other connections possible. Thus the dication of benzene has a (higher energy) isomer which is in fact a 4π antiaromatic species which avoids this antiaromaticity by a geometric distortion, with two C-H bonds bending above and below the ring. Such avoided antiaromaticity has been noted elsewhere here.

There is one final connection for me to make. My 2010 article[2] contained one of my interactive tables containing the data for the various structures (yes, although its data, you will need to have a subscription to the journal to access it). As it happens, last year we wished to reprise this style of publication, but as I blogged at the time, the journal had changed its production processes, and they could no longer offer me that opportunity. Some quick thinking came up with a replacement, which we now use extensively.[5] So the chain of connections resulting from that original talk some six years ago continues.

<

p>As for that chain, it arose distressingly randomly. I do not routinely read the entire ToC of JACS and so would not have discovered[4] the connection by that route. Fortunately, Steve Bachrach does and helped me make that connection to the molecule shown above. Although I did spend a few minutes thinking to myself “does that structure ring any bells?”. Fortunately, one did (eventually) ring. But for every connection made in this wonderfully human manner, I cannot help but think how many are not! However, if connections were much easier to make, could we as humans cope with the overwhelming deluge of new ideas?

References

  1. S. Pierrefixe, S. van Stralen, J. van Stralen, C. Fonseca Guerra, and F. Bickelhaupt, "Hypervalent Carbon Atom: “Freezing” the S<sub>N</sub>2 Transition State", Angewandte Chemie International Edition, vol. 48, pp. 6469-6471, 2009. https://doi.org/10.1002/anie.200902125
  2. H.S. Rzepa, "The rational design of helium bonds", Nature Chemistry, vol. 2, pp. 390-393, 2010. https://doi.org/10.1038/nchem.596
  3. C. Dohmeier, R. Köppe, C. Robl, and H. Schnöckel, "Kristallstruktur von [Cp★BBr][AlBr4]", Journal of Organometallic Chemistry, vol. 487, pp. 127-130, 1995. https://doi.org/10.1016/0022-328x(94)05089-t
  4. J. Jašík, D. Gerlich, and J. Roithová, "Probing Isomers of the Benzene Dication in a Low-Temperature Trap", Journal of the American Chemical Society, vol. 136, pp. 2960-2962, 2014. https://doi.org/10.1021/ja412109h
  5. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-García, M.J. Harvey, N.J. Mason, and H.S. Rzepa, "The Houk–List transition states for organocatalytic mechanisms revisited", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b

Tags:, , , , ,
Posted in Uncategorized | No Comments »

A connected world (journals and blogs): The benzene dication.

Thursday, April 10th, 2014

Science is rarely about a totally new observation or rationalisation, it is much more about making connections between known facts, and perhaps using these connections to extrapolate to new areas (building on the shoulders of giants, etc). So here I chart one example of such connectivity over a period of six years.

The story starts with this article[1], a preview talk about which (Hypervalent Carbon Atom: “Freezing” the SN2 Transition State) I actually saw at an ACS conference a year or so earlier. When the article was published, Steve Bachrach blogged about it, noting the claim for pentavalent carbon. The semantics of a valency vs a coordination are subtle, and I was not convinced that this frozen transition state deserved its elevation from penta-coordinate to pentavalent. After some discussion on Steve’s blog, I built upon these ideas with a few thoughts of my own on the present blog and then wondered whether they could be finally distilled into a more formal publication (testing the precedent in some ways of whether collaborative and public discussions of ideas could be published formally, or whether they would be rejected as having been already “published”). Well, these final distilled thoughts were indeed published in 2010[2], including their genesis in Steve’s blog (I wanted to put blogs more firmly into the acceptable scientific circle). This article included one species (numbered 5 in that article in 2010[2]) and pointed out an analogy to replacing CH2+ by e.g the isoelectronic BH1+, in as much as an example of the latter is indeed known as a stable crystalline compound.[3]. Iso-electronics is a very fruitful source of connections in chemistry!

5

Matters rested there until yesterday, when I spotted this on Steve’s blog where he discusses this recent article on the structure of the benzene dication.[4] Hey presto, there is that molecule again, but now there is firm experimental evidence of its existence! It was I think rather too much to expect the authors of this article to have spotted the connection to mine (although as it happens, both address the issue of complexes to He). The relationship between CH2+ and BH1+ is a little more subtle. From my point of view, it is always worth trawling through the crystal structure database in favour of evidence for hypothetical species (or their isoelectronic substitutions), and so it proved in this case!

There are other connections possible. Thus the dication of benzene has a (higher energy) isomer which is in fact a 4π antiaromatic species which avoids this antiaromaticity by a geometric distortion, with two C-H bonds bending above and below the ring. Such avoided antiaromaticity has been noted elsewhere here.

There is one final connection for me to make. My 2010 article[2] contained one of my interactive tables containing the data for the various structures (yes, although its data, you will need to have a subscription to the journal to access it). As it happens, last year we wished to reprise this style of publication, but as I blogged at the time, the journal had changed its production processes, and they could no longer offer me that opportunity. Some quick thinking came up with a replacement, which we now use extensively.[5] So the chain of connections resulting from that original talk some six years ago continues.

<

p>As for that chain, it arose distressingly randomly. I do not routinely read the entire ToC of JACS and so would not have discovered[4] the connection by that route. Fortunately, Steve Bachrach does and helped me make that connection to the molecule shown above. Although I did spend a few minutes thinking to myself “does that structure ring any bells?”. Fortunately, one did (eventually) ring. But for every connection made in this wonderfully human manner, I cannot help but think how many are not! However, if connections were much easier to make, could we as humans cope with the overwhelming deluge of new ideas?

References

  1. S. Pierrefixe, S. van Stralen, J. van Stralen, C. Fonseca Guerra, and F. Bickelhaupt, "Hypervalent Carbon Atom: “Freezing” the S<sub>N</sub>2 Transition State", Angewandte Chemie International Edition, vol. 48, pp. 6469-6471, 2009. https://doi.org/10.1002/anie.200902125
  2. H.S. Rzepa, "The rational design of helium bonds", Nature Chemistry, vol. 2, pp. 390-393, 2010. https://doi.org/10.1038/nchem.596
  3. C. Dohmeier, R. Köppe, C. Robl, and H. Schnöckel, "Kristallstruktur von [Cp★BBr][AlBr4]", Journal of Organometallic Chemistry, vol. 487, pp. 127-130, 1995. https://doi.org/10.1016/0022-328x(94)05089-t
  4. J. Jašík, D. Gerlich, and J. Roithová, "Probing Isomers of the Benzene Dication in a Low-Temperature Trap", Journal of the American Chemical Society, vol. 136, pp. 2960-2962, 2014. https://doi.org/10.1021/ja412109h
  5. A. Armstrong, R.A. Boto, P. Dingwall, J. Contreras-García, M.J. Harvey, N.J. Mason, and H.S. Rzepa, "The Houk–List transition states for organocatalytic mechanisms revisited", Chem. Sci., vol. 5, pp. 2057-2071, 2014. https://doi.org/10.1039/c3sc53416b

Tags:, , ,
Posted in Hypervalency, Interesting chemistry | No Comments »

« Older Entries