Posts Tagged ‘chemical shift’

Hypervalent Helium – not!

Friday, February 16th, 2018

Last year, this article[1] attracted a lot of attention as the first example of molecular helium in the form of Na2He. In fact, the helium in this species has a calculated‡ bond index of only 0.15 and it is better classified as a sodium electride with the ionisation induced by pressure and the presence of helium atoms. The helium is neither valent, nor indeed hypervalent (the meanings are in fact equivalent for this element). In a separate blog posted in 2013, I noted a cobalt carbonyl complex containing a hexacoordinate hydrogen in the form of hydride, H–. A comment appended to this blog insightfully asked about the isoelectronic complex containing He instead of H–. Here, rather belatedly, I respond to this comment!

The complex [HCo6(CO)15]– has a calculated bond index at the hydrogen of 0.988 and a calculated NMR chemical shift of 21.6 ppm (ωB97XD/Def2-TZVPPD calculation) compared to a measured value of 23.2 ppm. Despite being six-coordinate, the hydride has a bond index that does not exceed one (it is not hypervalent).

So here is the neutral helium analogue. The He bond index emerges as 0.71 at the geometry of the hydride complex. Compare this with the bond index of 0.15 calculated for Na2He and it would be fair to say that at this geometry, the helium in [HeCo6(CO)15] would have a greater claim to be a molecular compound. Back in 2010, extrapolating from a series of posts here, I had speculated[2] about other molecular species of He, including the di-cation below. This has a He bond index of 0.54, rather less than that in [HeCo6(CO)15] but much more than in Na2He. It is also vibrationally stable.

But now, [HeCo6(CO)15] goes “pear-shaped” (why do pears have such a bad press?). I started a process of optimizing the geometry of this complex (ωB97Xd/Def2-TZVPPD). Slowly, the He started to creep out of the centre of the complex and emerge from the cavity. After about 100 steps it reached the geometry shown below, at which point the Wiberg bond index has dropped to 0.62 and still going down. I think it might take a few more steps to be completely expelled, but I have stopped the geometry optimisation at this stage.

So helium appears not to be valent in [HeCo6(CO)15]. However, I have yet to try Ne, which is both larger and softer. I will post results here.

‡All data at 10.14469/hpc/3587.

References

  1. X. Dong, A.R. Oganov, A.F. Goncharov, E. Stavrou, S. Lobanov, G. Saleh, G. Qian, Q. Zhu, C. Gatti, V.L. Deringer, R. Dronskowski, X. Zhou, V.B. Prakapenka, Z. Konôpková, I.A. Popov, A.I. Boldyrev, and H. Wang, "A stable compound of helium and sodium at high pressure", Nature Chemistry, vol. 9, pp. 440-445, 2017. https://doi.org/10.1038/nchem.2716
  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

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Posted in Hypervalency | 4 Comments »

Hypervalent hydrogen?

Saturday, January 13th, 2018

I discussed the molecule the molecule CH3F2- a while back. It was a very rare computed example of a system where the added two electrons populate the higher valence shells known as Rydberg orbitals as an alternative to populating the C-F antibonding σ-orbital to produce CH3– and F–. The net result was the creation of a weak C-F “hyperbond”, in which the C-F region has an inner conventional bond, with an outer “sheath” encircling the first bond. But this system very easily dissociates to CH3– and F– and is hardly a viable candidate for experimental detection.  In an effort to “tune” this effect to see if a better candidate for such detection might be found, I tried CMe3F2-. Here is its story.

The calculation‡ is at the ωB97XD/Def2-TZVPPD/SCRF=water level (water is here used as an approximate model for a condensed environment, helping to bind the two added electrons).

  1. An NBO (Natural Bond orbital) analysis reveals a total Rydberg orbital population of 1.186e and the following bond indices; F 0.853, C 3.977, C(methyl) 4.051, H(*3) 1.332. The latter corresponds to the three methyl hydrogens aligned antiperiplanar to the C-F bond.
  2. To put this value into context, the hydrogen in the FHF– anion has an NBO H bond index of 0.724, and the bridging hydrogens in diborane only have a value of 0.988. Even the hexa-coordinate hydride system [Co6H(CO)15]– discussed in an earlier blog  has an H bond index of just 0.86. Actually, coordination of six or even higher for hydrogen is no longer rare; some 28 crystal structures of the type HM6 (M=metal) are known (it would be useful to find out if any of the other 27 such structures might have a hydrogen bond index >1).
  3. Next, the ELF analysis (Electron localisation function), analysed firstly using the excellent MultiWFN program.[1]

    This reveals an attractor basin integrating to 1.663e and located along the axis of the F-C bond and extended into the region of the three antiperiplanar methyl hydrogens. The C-F bond itself only supports a basin of 0.729e, typical of the fairly ionic C-F bond. The covalent C-Me bonds are also pretty normal, as are the other hydrogens.
  4. I also show ELF analysis using the alternative TopMod program[2]; the numerical values on this diagram are the calculated bond lengths in Å. The basin integrations are very similar to those obtained using MultiWFN.

    The Wiberg bond orders of the three H…H regions shown connected by dashed lines above are 0.154, which contributes to the bond index of >1 at these three hydrogens.
  5. The predicted 1H chemical shift of these three “hypervalent” hydrogens is +3.0 ppm, whilst the other six methyl hydrogens are at -0.87ppm.

So changing CH3F2- to CMe3F2- has dramatically changed the bonding picture that emerges, rather than a fine-tuning. The C-F is no longer a “hyperbond”, although the Rydberg occupancy of 1.186e remains unusually large. Most of the additional electrons have fled the torus surrounding the C-F bond and relocated to the exo-region of that bond where they now influence the three antiperiplanar methyl hydrogens. A two-electron-three-centre interaction if you like, but with the electron basin occupying a tetrahedral vertex rather than the triatom centroid.

I end with a challenge. Is it possible to find “real” molecules containing hydrogen where the formal bond index for at least one hydrogen exceeds 1.0 significantly, thus making it hypervalent? 

‡The calculations are all collected at FAIR doi; 10.14469/hpc/3372.

References

  1. T. Lu, and F. Chen, "Multiwfn: A multifunctional wavefunction analyzer", Journal of Computational Chemistry, vol. 33, pp. 580-592, 2011. https://doi.org/10.1002/jcc.22885
  2. S. Noury, X. Krokidis, F. Fuster, and B. Silvi, "Computational tools for the electron localization function topological analysis", Computers & Chemistry, vol. 23, pp. 597-604, 1999. https://doi.org/10.1016/s0097-8485(99)00039-x

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Posted in Hypervalency | 2 Comments »

Dispersion “bonds”: a new example with an ultra-short H…H distance.

Monday, June 26th, 2017

About 18 months ago, there was much discussion on this blog about a system reported by Bob Pascal and co-workers containing a short H…H contact of ~1.5Å[1]. In this system, the hydrogens were both attached to Si as Si-H…H-Si and compressed together by rings. Now a new report[2] and commented upon by Steve Bachrach, claims a similar distance for hydrogens attached to carbon, i.e. C-H…H-C, but without the ring compression.

This new example is the structure of an C3-symmetric all-meta tBu-triphenylmethane R-H…H-R dimer determined by neutron diffraction (DOI: 10.5517/ccdc.csd.cc1nc1bd) and the close interaction is achieved purely by attractions due to dispersion forces accumulating in the remainder of the molecules. This study also reports a diverse set of computed properties for this new system, but one property reported as part of the previous discussion was not presented, the 1JH-H coupling constant. I have computed it here in the hope that it might be possible to measure by some means, perhaps in the solid state?

The chemical shift of the R3CH proton is measured as a singlet‡ at ~7.35 ppm (in deuterated benzene, Figure S6, SI).† 

The value calculated using B3LYP/Def2-TZVPP (gas phase) is 7.39 and 7.69 ppm (averaged to 7.54 for a rapidly exchanging environment). The 1J coupling is calculated as 4.3 Hz at the B3LYP/Def2-TZVPP level, DOI: 10.14469/hpc/2699. The designation 1J is normally taken as a 1-bond pathway for the coupling. In this example, the designation of the H-H region as a “bond” is the interesting discussion point!

I end by noting here my observation that although the neutron diffraction study of ammonium tetraphenylborate shows the  N-H protons as pointing directly towards the centroid of phenyl groups, the original observation[3] was made that “even at 20 K the ammonium ion performs large amplitude motions which allow the N-H vectors to sample the entire face of the aromatic system”.  The equivalent thermal motion for the triphenylmethane system here would have the  C-H vectors orbiting around each other in a manner that increases the H-H separation, but which averages out to them pointing directly towards one another?  The calculated normal coordinate analysis of this system is not available from the article SI, so the ease of  C-C-H bending to achieve such motion is difficult to ascertain. Perhaps trying to detect the 1J coupling might illuminate whether this happens?

Postscript. †Prof Schreiner has indicated that that the methine assignment is 5.79 ppm (b below) and not 7.35 as marked with a diamond in the S6 figure caption (a below). This is of course measured in d6-benzene solution and applies to the monomer, not presumably the dimer. The calculated value of 7.54 ppm as reported above applies specifically to the dimer, which suggests a significant shift of ~2ppm upon dimer formation. It would be interesting to verify this prediction via a solid-state measurement.

‡Measuring coupling would require an asymmetric environment to differentiate the two chemical shifts of the interacting hydrogens. Although the C3 symmetry of the crystal structure could provide such an environment, it is observed to be fluxional in solution,  which equalises the two chemical shifts on the NMR time scale. Two non-equivalent protons exhibiting only mutual couplings manifest as an AB-type double doublet of peaks in the NMR spectrum. As the difference in chemical shift between the two nuclei (in units of Hz) approaches in magnitude the value of the coupling constant between them (also in Hz), the AB quartet becomes increasingly second-order in appearance. This means that the intensities of the two outer peaks starts to decrease and the two inner peak intensities increase. When the chemical shift difference between them reaches zero, the intensity of the two outer peaks also becomes zero and the two inner peaks superimpose to become a single peak. This means that the coupling constant cannot be measured from the splitting of the peaks (which has vanished). It does not mean of course that the coupling itself has vanished; it merely no longer manifests in the spectrum.

References

  1. J. Zong, J.T. Mague, and R.A. Pascal, "Exceptional Steric Congestion in an <i>in</i>,<i>in</i>-Bis(hydrosilane)", Journal of the American Chemical Society, vol. 135, pp. 13235-13237, 2013. https://doi.org/10.1021/ja407398w
  2. S. Rösel, H. Quanz, C. Logemann, J. Becker, E. Mossou, L. Cañadillas-Delgado, E. Caldeweyher, S. Grimme, and P.R. Schreiner, "London Dispersion Enables the Shortest Intermolecular Hydrocarbon H···H Contact", Journal of the American Chemical Society, vol. 139, pp. 7428-7431, 2017. https://doi.org/10.1021/jacs.7b01879
  3. T. Steiner, and S.A. Mason, "Short N<sup>+</sup>—H...Ph hydrogen bonds in ammonium tetraphenylborate characterized by neutron diffraction", Acta Crystallographica Section B Structural Science, vol. 56, pp. 254-260, 2000. https://doi.org/10.1107/s0108768199012318

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Posted in Interesting chemistry | 3 Comments »

Dispersion "bonds": a new example with an ultra-short H…H distance.

Monday, June 26th, 2017

About 18 months ago, there was much discussion on this blog about a system reported by Bob Pascal and co-workers containing a short H…H contact of ~1.5Å[1]. In this system, the hydrogens were both attached to Si as Si-H…H-Si and compressed together by rings. Now a new report[2] and commented upon by Steve Bachrach, claims a similar distance for hydrogens attached to carbon, i.e. C-H…H-C, but without the ring compression.

This new example is the structure of an C3-symmetric all-meta tBu-triphenylmethane R-H…H-R dimer determined by neutron diffraction (DOI: 10.5517/ccdc.csd.cc1nc1bd) and the close interaction is achieved purely by attractions due to dispersion forces accumulating in the remainder of the molecules. This study also reports a diverse set of computed properties for this new system, but one property reported as part of the previous discussion was not presented, the 1JH-H coupling constant. I have computed it here in the hope that it might be possible to measure by some means, perhaps in the solid state?

The chemical shift of the R3CH proton is measured as a singlet‡ at ~7.35 ppm (in deuterated benzene, Figure S6, SI).† 

The value calculated using B3LYP/Def2-TZVPP (gas phase) is 7.39 and 7.69 ppm (averaged to 7.54 for a rapidly exchanging environment). The 1J coupling is calculated as 4.3 Hz at the B3LYP/Def2-TZVPP level, DOI: 10.14469/hpc/2699. The designation 1J is normally taken as a 1-bond pathway for the coupling. In this example, the designation of the H-H region as a “bond” is the interesting discussion point!

I end by noting here my observation that although the neutron diffraction study of ammonium tetraphenylborate shows the  N-H protons as pointing directly towards the centroid of phenyl groups, the original observation[3] was made that “even at 20 K the ammonium ion performs large amplitude motions which allow the N-H vectors to sample the entire face of the aromatic system”.  The equivalent thermal motion for the triphenylmethane system here would have the  C-H vectors orbiting around each other in a manner that increases the H-H separation, but which averages out to them pointing directly towards one another?  The calculated normal coordinate analysis of this system is not available from the article SI, so the ease of  C-C-H bending to achieve such motion is difficult to ascertain. Perhaps trying to detect the 1J coupling might illuminate whether this happens?

Postscript. †Prof Schreiner has indicated that that the methine assignment is 5.79 ppm (b below) and not 7.35 as marked with a diamond in the S6 figure caption (a below). This is of course measured in d6-benzene solution and applies to the monomer, not presumably the dimer. The calculated value of 7.54 ppm as reported above applies specifically to the dimer, which suggests a significant shift of ~2ppm upon dimer formation. It would be interesting to verify this prediction via a solid-state measurement.

‡Measuring coupling would require an asymmetric environment to differentiate the two chemical shifts of the interacting hydrogens. Although the C3 symmetry of the crystal structure could provide such an environment, it is observed to be fluxional in solution,  which equalises the two chemical shifts on the NMR time scale. Two non-equivalent protons exhibiting only mutual couplings manifest as an AB-type double doublet of peaks in the NMR spectrum. As the difference in chemical shift between the two nuclei (in units of Hz) approaches in magnitude the value of the coupling constant between them (also in Hz), the AB quartet becomes increasingly second-order in appearance. This means that the intensities of the two outer peaks starts to decrease and the two inner peak intensities increase. When the chemical shift difference between them reaches zero, the intensity of the two outer peaks also becomes zero and the two inner peaks superimpose to become a single peak. This means that the coupling constant cannot be measured from the splitting of the peaks (which has vanished). It does not mean of course that the coupling itself has vanished; it merely no longer manifests in the spectrum.

References

  1. J. Zong, J.T. Mague, and R.A. Pascal, "Exceptional Steric Congestion in an <i>in</i>,<i>in</i>-Bis(hydrosilane)", Journal of the American Chemical Society, vol. 135, pp. 13235-13237, 2013. https://doi.org/10.1021/ja407398w
  2. S. Rösel, H. Quanz, C. Logemann, J. Becker, E. Mossou, L. Cañadillas-Delgado, E. Caldeweyher, S. Grimme, and P.R. Schreiner, "London Dispersion Enables the Shortest Intermolecular Hydrocarbon H···H Contact", Journal of the American Chemical Society, vol. 139, pp. 7428-7431, 2017. https://doi.org/10.1021/jacs.7b01879
  3. T. Steiner, and S.A. Mason, "Short N<sup>+</sup>—H...Ph hydrogen bonds in ammonium tetraphenylborate characterized by neutron diffraction", Acta Crystallographica Section B Structural Science, vol. 56, pp. 254-260, 2000. https://doi.org/10.1107/s0108768199012318

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Posted in Interesting chemistry | 3 Comments »

Conference report: OPEN SCIENCE AND THE CHEMISTRY LAB OF THE FUTURE

Tuesday, May 23rd, 2017

This is taking place in the idyllic surroundings of the Niederwald forest, Rüdesheim, Germany. Here I highlight only aspects of the first three talks.

Martin Hicks introduced the conference with concepts such as the global public good. In the area of open access, he reminded us of the terms Platinum/Diamond open access, which are journals with no article processing charges (which can reach £5000 per article for some other OA journals), but which go with the challenge of ensuring that more gatekeepers of this global public good are needed to avoid being overwhelmed. He ended by asking us all to consider what  the unit of knowledge is that needs to be shared.

The first talk was by Klaus Tochtermann who (amongst other topics) brought to our attention the Dutch GoFAIR initiative  in the European Open Science Cloud, sub-divided into Go-train (i.e. data experts, who will build e.g. metadata tools) and Go-build (eco-systems: Internet of FAIR data and FAIR services). I think the message is that all organisations with chemistry labs should consider this as being an essential part of their future infrastructures.

Jeremy Frey’s title was Reducing Uncertainty: The Raison d’Être for Open Science who defined the fundamental principles of open science as transparency, capability and obtainability and encouraged data publication at source (as opposed to e.g. PhD writing up period) to ensure fidelity in the capture of metadata.

The team of Leah McEwen, Ian Bruno, Stuart Chalk and Richard Kidd told us about Global Data Initiatives and Chemistry and the need for social and technical bridges to enable open data sharing. I learnt for example that the IUPAC Gold book of chemical terms and definitions now has DOIs for each of the terms. Thus chemical shift (DOI: 10.1351/goldbook.C01036[1]), spectroscopy (DOI: 10.1351/goldbook.S05848[2]) and electron density function (DOI: 10.1351/goldbook.ET07024[3]). I will now to associate such links with e.g. deposited NMR data to help increase the semantics of the data (see e.g. DOI: 10.14469/hpc/1975).

Finally, a photo from the region, taken from the gondola adjacent to the venue and riding down to the small town on the banks of the Rhine.

References

  1. "chemical shift", The IUPAC Compendium of Chemical Terminology, 2014. https://doi.org/10.1351/goldbook.c01036
  2. "spectroscopy", The IUPAC Compendium of Chemical Terminology, 2014. https://doi.org/10.1351/goldbook.s05848
  3. "electron density function", The IUPAC Compendium of Chemical Terminology, 2014. https://doi.org/10.1351/goldbook.et07024

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Posted in Chemical IT | 1 Comment »

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

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Posted in pericyclic, reaction mechanism | 5 Comments »

Hexacoordinate hydrogen.

Monday, July 8th, 2013

A feature of a blog which is quite different from a journal article is how rapidly a topic might evolve. Thus I started a few days ago with the theme of dicarbon (C2), identifying a metal carbide that showed C2 as a ligand, but which also entrapped a single carbon in hexa-coordinated mode. A comment was posted bringing attention to the origins of the discovery of hexacoordinated carbon, and we moved on to exploring the valency in one such species (CLi6). Here I ask if hydrogen itself might exhibit such coordination.

Click for 3D.

Click for 3D.

In fact, such a system was first reported as long ago as 1981[1]. This contains a cobalt carbonyl anion of the type [Co6H(CO)15]–. The hexacoordinated hydrogen had a measured 1H NMR chemical shift of 23.2 ppm (very low field), a value normally more associated with a proton rather than a hydride.

What does quantum mechanics say about this system? The QTAIM (ωB97XD/6=311G(d,p) calculation[2]) is shown below. The green spheres represent bond critical points, and indeed six surround the central hydrogen with octahedral coordination. The value of ρ(r) for these varies from 0.074 to 0.082 au, which is a higher electron density than might be found for e.g. a hydrogen bond (which is typically 0.020 – 0.010 au). The individual Co…H Wiberg bond order indices are ~0.1 (the total Wiberg bond index is 0.86).

Co6H-QTAIM

The computed 1H chemical shift[3] (relative to TMS) of the hydrogen is 30.8 ppm, which seems to agree with an interpretation based on a proton in the interstitial cavity. However, the NBO natural charge on this hydrogen is -0.41, for a valence population of 1.40 electrons (and a Rydberg population of 0.01), which makes it more of a hydride anion than a cationic proton. NBO characterises this electron population as “Lp” (Lone pair). One might conclude from these apparently opposed indications that the deshielding of the 1H is less to do with its resemblance to a proton, and is more due to the local magnetic currents originating from the metal atoms.

It is still nicely surprising that even an element as small as hydrogen can sustain hexa-coordination. It also reminds that although each of the coordinations is via what can reasonably be called a bond, the hydrogen nevertheless does not exceed its maximum valence electron shell electron count of two;  in that sense it is not hypervalent.

References

  1. D.W. Hart, R.G. Teller, C. Wei, R. Bau, G. Longoni, S. Campanella, P. Chini, and T.F. Koetzle, "An interstitial hydrogen atom in a hexanuclear metal cluster: x-ray and neutron diffraction analysis of [(Ph3P)2N]+[HCo6(CO)15]-", Journal of the American Chemical Society, vol. 103, pp. 1458-1466, 1981. https://doi.org/10.1021/ja00396a028
  2. H.S. Rzepa, "Gaussian Job Archive for C15HCo6O15(1-)", 2013. https://doi.org/10.6084/m9.figshare.741232
  3. "C 15 H 1 Co 6 O 15 -1", 2013. http://hdl.handle.net/10042/24804

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Posted in Hypervalency, Interesting chemistry | 2 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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