Posts Tagged ‘Oxygen’

The di-anion of dilithium (not the Star Trek variety): Another “Hyper-bond”?

Saturday, September 16th, 2017

Early in 2011, I wrote about how the diatomic molecule Be2 might be persuaded to improve upon its normal unbound state (bond order ~zero) by a double electronic excitation to a strongly bound species. I yesterday updated this post with further suggestions and one of these inspired this follow-up.

The standard molecular orbital diagram for Be2 below shows two electrons in both the 2s Σg and Σu levels, the first being considered bonding and the second antibonding. By exciting the two electrons from the Σu into the Πu MO to form a triplet, one converts one antibonding occupancy into two bonding occupancies, in the process changing the total formal bond order from zero to two.

 

The triplet excited state of diberyllium

You can see the results of my playing with these ideas both in my appended comments to the original post and the table below. This shows that the calculated bond order for the excited triplet state of Be2 is actually closer to 1.50 rather than to two, but definitely not zero!

System Wiberg bond order Bond length FAIR Data
Be2 singlet 0.15 2.805 10.14469/hpc/3082
Be2 excited triplet 1.50 1.785 10.14469/hpc/3075
Be22+ 1.00 2.135 10.14469/hpc/3076
Be22- triplet 0.89 2.242 10.14469/hpc/3074
Be22- excited singlet 3.00 1.817 10.14469/hpc/3083

The games above represent isoelectronic substitutions and here I try one more, namely that Li22- is isoelectronic with Be2. Unlike the latter, there is no need to force an electronic excitation (ωB97XD/Def2-QZVPPD/SCRF=water) to achieve the required occupancies with Li22-.

System Wiberg bond order Bond length FAIR Data
Li22- triplet 1.501 2.381 10.14469/hpc/3087

I also checked what crystal structures could tell us about Li-Li bonds and it seems 2.38Å is about as short as they get.

At this point, the NBO analysis of the Li22- localised orbitals alerted me to another feature, which is that the Rydberg occupancy amounted to 2.18e. This in turn reminded me of the previous post which dealt with such occupancy in another small molecule, CH3F2-, but here the Rydberg occupancy involved the 3s/3p AOs of the carbon and the fluorine. With Li22- triplet, it is of the lithium 2p AO (2.18e) and only a tiny occupancy of 3d (0.03). By definition, for alkali metals such as Li the normal valence shell is just 2s, whereas 2p occupancy is considered a Rydberg state; a hypervalent state if you will. So Li22- triplet has a Li-Li hyper-bond!‡ Of course, by this definition most Li compounds are then hypervalent, since many have populated 2p shells.

Even if use of the term hyper-bond to describe Li22- triplet is rather artificial, this example does reveal the games one can play with the first row elements Li-B (see table above). Given that most introductory text books on bonding normally only explain the diatomics formed from N-Ne (occasionally including C), I might suggest that these earlier elements are equally instructive and fun to play with.

‡ This species is 36.0 kcal/mol higher in free energy than two separated Li– anions.

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Posted in Interesting chemistry | 3 Comments »

The di-anion of dilithium (not the Star Trek variety): Another "Hyper-bond"?

Saturday, September 16th, 2017

Early in 2011, I wrote about how the diatomic molecule Be2 might be persuaded to improve upon its normal unbound state (bond order ~zero) by a double electronic excitation to a strongly bound species. I yesterday updated this post with further suggestions and one of these inspired this follow-up.

The standard molecular orbital diagram for Be2 below shows two electrons in both the 2s Σg and Σu levels, the first being considered bonding and the second antibonding. By exciting the two electrons from the Σu into the Πu MO to form a triplet, one converts one antibonding occupancy into two bonding occupancies, in the process changing the total formal bond order from zero to two.

 

The triplet excited state of diberyllium

You can see the results of my playing with these ideas both in my appended comments to the original post and the table below. This shows that the calculated bond order for the excited triplet state of Be2 is actually closer to 1.50 rather than to two, but definitely not zero!

System Wiberg bond order Bond length FAIR Data
Be2 singlet 0.15 2.805 10.14469/hpc/3082
Be2 excited triplet 1.50 1.785 10.14469/hpc/3075
Be22+ 1.00 2.135 10.14469/hpc/3076
Be22- triplet 0.89 2.242 10.14469/hpc/3074
Be22- excited singlet 3.00 1.817 10.14469/hpc/3083

The games above represent isoelectronic substitutions and here I try one more, namely that Li22- is isoelectronic with Be2. Unlike the latter, there is no need to force an electronic excitation (ωB97XD/Def2-QZVPPD/SCRF=water) to achieve the required occupancies with Li22-.

System Wiberg bond order Bond length FAIR Data
Li22- triplet 1.501 2.381 10.14469/hpc/3087

I also checked what crystal structures could tell us about Li-Li bonds and it seems 2.38Å is about as short as they get.

At this point, the NBO analysis of the Li22- localised orbitals alerted me to another feature, which is that the Rydberg occupancy amounted to 2.18e. This in turn reminded me of the previous post which dealt with such occupancy in another small molecule, CH3F2-, but here the Rydberg occupancy involved the 3s/3p AOs of the carbon and the fluorine. With Li22- triplet, it is of the lithium 2p AO (2.18e) and only a tiny occupancy of 3d (0.03). By definition, for alkali metals such as Li the normal valence shell is just 2s, whereas 2p occupancy is considered a Rydberg state; a hypervalent state if you will. So Li22- triplet has a Li-Li hyper-bond!‡ Of course, by this definition most Li compounds are then hypervalent, since many have populated 2p shells.

Even if use of the term hyper-bond to describe Li22- triplet is rather artificial, this example does reveal the games one can play with the first row elements Li-B (see table above). Given that most introductory text books on bonding normally only explain the diatomics formed from N-Ne (occasionally including C), I might suggest that these earlier elements are equally instructive and fun to play with.

‡ This species is 36.0 kcal/mol higher in free energy than two separated Li– anions.

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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 »

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 »

Na2He: a stable compound of helium and sodium at high pressure.

Saturday, February 11th, 2017

On February 6th I was alerted to this intriguing article[1] by a phone call, made 55 minutes before the article embargo was due to be released. Gizmodo wanted to know if I could provide an (almost)† instant‡ quote. After a few days, this report of a stable compound of helium and sodium still seems impressive to me and I now impart a few more thoughts here.

The discovery originates from 17 authors based in 17 different institutions, an impressive illustration of global science and cooperation. I illustrate with this diagram, to be found not in the main article body but in its supporting information and for which the caption reads:


Computed charge density (eÅ-3) of Na2He at 300 GPa, plotted in the [110] plane of the conventional cell. The color bar gives the scale.

The nuclei carry of course the greatest charge density, but the density labelled “2e” is not nuclear-centered. This is typical of species known as electrides, where positive cations are associated with just electrons acting as the counter-anion and about which there was an extensive debate earlier on this blog. There is much discussion in the article[1] about the essential role of the He atoms in bringing about the formation of such an electride, an effect that is summarised in a second diagram also found in the supporting information:

I found myself thinking that it would be great to have the first diagram represented as a movie, evolving as the pressure is increased from say ambient to 300 GPa, and presumably showing the “2e” feature (which means diamagnetic electrons) forming as the pressure increases. Would their evolution be abrupt (a step change) or gradual as the pressure increases and the interatomic distances all decrease? As I understand it, this chemical phenomenon is due not so much to the usual coulombic attraction between positive nuclei and negative charge density from the electronic wavefunction leading to e.g. covalent bonds, but to electron repulsions induced by decreasing nuclear separations resulting in electride-like ionisation and hence electron localisation into the “interstitial cavities” of the lattice. Without pressure, you would just have sodium and helium atoms!

The urge to obtain this intriguing electronic wavefunction for myself now appeared (wavefunctions are rarely if ever included in supporting information). To do this you must have atom coordinates available, But such data was not to be found in the supporting information. It was eventually tracked down (by a crystallographer; thanks Andrew!) to the caption in Figure 2.

However, you probably do need to be a crystallographer to convert this data into a set of coordinates. This was done and is here deposited as a CIF file for you to play with if you wish (DOI:10.14469/hpc/2154)[2]. I have reduced the packing of the unit cell obtained from this CIF file (198 atoms) to just 60 and you can enjoy them by clicking on the diagram below. I should point out that if one uses a program that can recognise the periodic lattice such as Crystal (used in the article discussed here), there is no need to make such reductions, but in this instance I wanted to use a program such as Gaussian in discrete (non-periodic) mode, for which the calculation (B3LYP/Def2-SVPD) has DOI: 10.14469/hpc/2156[3] and where you can also find a wavefunction file to play with if you wish.

Click for 3D model

An ELF analysis for this non-periodic wavefunction looks as below. The ELF basins labelled “2e” located in the centre of the cube show an integrated electron population of ~1.9e and correspond to the localised electron pairs noted in the article above.

Click for 3D

The basins on the boundaries of this non-periodic unit show reduced integrations (red arrows below, 0.08 – 1.7e) and are artefacts of the non-periodic approximation introduced.

The ionization into an electride is brought about by the close proximity of the atoms as induced by high pressure. Releasing the pressure would allow the ionized electrons to re-attach themselves to the valence shell of the sodium atoms, thus destroying the unique properties of the system. It is certainly true that this system challenges our normal concepts of what a molecule is. The presence of He is essential and yet its electrons are hardly involved in the re-organised wavefunction. I cannot wait for more examples to be discovered!

†To meet the 55 minute deadline, I was given about 15 minutes thinking time!

‡Instant responses on social media now seem a sine qua non of the political world, so why not the scientific one?!

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. Rzepa, "Na2He: a stable compound of helium and sodium at high pressure.", 2017. https://doi.org/10.14469/hpc/2154
  3. H. Rzepa, "He20Na40", 2017. https://doi.org/10.14469/hpc/2156

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Posted in Bond slam, crystal_structure_mining, Interesting chemistry | 11 Comments »

Allotropic halogens.

Sunday, April 26th, 2015

Allotropes are differing structural forms of the elements. The best known example is that of carbon, which comes as diamond and graphite, along with the relatively recently discovered fullerenes and now graphenes. Here I ponder whether any of the halogens can have allotropes.

Firstly, I am not aware of much discussion on the topic. But ClF3 is certainly well-known, and so it is trivial to suggest BrBr3, i.e. Br4 as an example of a halogen allotrope. Scifinder for example gives no literature hits on such a substance (either real or as a calculation; it is not always easy nowadays to tell which). So, is it stable? A B3LYP+D3/6-311++G(2d,2p) calculation reveals a free energy barrier of 17.2 kcal/mol preventing Br4 from dissociating to 2Br2.[1] The reaction however is rather exoenergic, and so to stand any chance of observing Br4, one would probably have to create it at a low temperature. But say -78° would probably be low enough to give it a long lifetime; perhaps even 0°.

Br4c
Br4

So how to make it? This is pure speculation, but the red colour of bromine originates from (weak, symmetry forbidden) transitions, with energies calculated (for the 2Br2 complex) as 504, 492nm. Geometry optimisation of the first singlet excited state of 2Br2 produces the structure below, not that different from Br4.
2Br2-excited

 

At least from these relatively simple calculations, it does seem as if an allotrope of bromine might be detectable spectroscopically, if not actually isolated as a pure substance.

References

  1. H.S. Rzepa, "Br4", 2015. https://doi.org/10.14469/ch/191228

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Posted in reaction mechanism | 11 Comments »