Archive for the ‘Bond slam’ Category

Two new types in the chemical bonding zoo: exo-bonds and hyper-bonds?

Wednesday, September 6th, 2017

The chemical bond zoo is relatively small (the bond being a somewhat fuzzy concept, I am not sure there is an actual count of occupants). So when two new candidates come along, it is worth taking notice. I have previously noted the Chemical Bonds at the 21st Century-2017: CB2017 Aachen conference, where both were discussed.

  1. The first now has a name, the exo-bond, one example of which is the C2 diatomic. The hint that a quadruple bond could be formulated between the two carbon atoms goes back a little while[1] (see Table 1), but revived interest really took off after ~2010, around the time my blog on the topic also appeared. You can see the abundance of post 2010 articles in the bibliography at the Aachen bond-slam. At the conference, four speakers all agreed using rather different methods that there was indeed “something” additional to a C≡C triple bond and that this “something” might be worth ~15-30 kcal/mol of stabilization. The debate centered around whether this term deserved to be called a bond, or whether it should be downgraded to merely that of biradicaloid stabilizations. The more conventional population of a σ*-antibond it was argued would not result in such stabilizations. Since many kinds of bonds have stabilization energies of similar magnitude, not least the weaker hydrogen bonds, agostic bonds, halogen bonds etc, let us for the sake of argument call it a bond here. Because four electrons might occupy the same space along the σ-symmetric C-C axis, they experience significant so-called static correlation which results in partition into one electron pair occupying the central region (the endo-bond) and the other pair in the outer region (the exo-bond).  This separation decreases the Pauli electron repulsions along the entire C-C axis region.  An example of an exo-bond is found in [1.1.1] propellane, where the notional central C-C bond is thought to actually occupy the region outside the central C-C bond axis, but largely in this example because of angular strains. In this case however, the propellane bond is not competing with an endo-bond along the same axis. We might conclude therefore that the convention of characterising a bond using the separation between the two nuclei (the bond-length) is rather stressed when one has two different bonds along the axis of the nuclei, one of which is obviously “longer” than the other.

    Which brings us to representations; e.g. Chemdraw now allows drawing of quadruple bonds and so it can be drawn thus quite simply.

    The second form breaks the century-old convention that all bonds along a diatomic axis are drawn in the same manner, by isolating the exo-bond to make the point clear. Perhaps we should stick to the first, but be prepared to explain the underlying complexity of the quantum mechanical symmetries as we do to students with σ/π/δ/φ bonds, which are another mechanism for avoiding having bonds in exactly the same regions. I know the story has not yet ended; but is it time to at least speculate when the text-books will start to reflect/discuss the exo-bond?

  2. The second I dub the hyper-bond. This goes back to G. N. Lewis and his famous octet rule for main group elements, the expansion of which was subsequently described by the term hypervalent. That term has become rather confused with hypercoordinate, since hypervalent is often used to describe hypercoordinate species such as PCl5, SF6 or I.I7. But this does rather break the original definition, since few if indeed any of these hypercoordinate molecules have a significantly expanded octet shell. At the Aachen meeting, a molecule fitting the original definition was presented, appearing first in early form on this blog. Put simply, a wavefunction for CH3F2- can be calculated (ωB97XD/Def2-QZVPPD/SCRF=water, DOI: cb3n ) for which the two additional electrons populate a molecular orbital with significant contributions from the 3s/3p valence shell AOs (atomic orbitals) for both carbon and fluorine. The alternative would have been to populate the anti-bonding C-H or C-F orbitals composed of 2s/2p valence shell AOs. The former results in a total population of these higher valence shells of 1.55e and makes the C-F (Wiberg) bond order >1 (1.14) and the total Wiberg bond indices >4 for carbon (4.162) and >1 for F (1.275). The resulting HOMO (highest occupied molecular orbital) or NBO (they are very similar) looks as below. It takes the approximate form of a torus or cylinder wrapping the inner C-F bond, a second layer to the C-F bond if you wish. 

    Normal valence shell F-C σ-orbital defining the regular C-F bond.

    Higher valence shell F-C σ-orbital defining the C-F hyper-bond.

    Rather than the entire molecule being defined as hypervalent, only one (in this case localized) orbital is given the term and the other orbitals are conventional.

In both cases the molecules are either very reactive (C2) or with such a low barrier to fragmentation (into CH3 and F for CH3F2-) that detection of the latter is unlikely. But these are interesting Gedanken experiments in quantum mechanics, which in turn catalyse the development of new techniques and in some cases might even lead to the design and isolation of new types of molecules.


The known thermochemistry of the two reactions; HC≡CH → HC≡C + H•; HC≡C• → CC + H• is ~17 kcal/mol less endothermic for the second step, suggesting some factor is needed to account for the additional stabilization when CC is formed.

The singlet to triplet excitation energy for C2 is ~+30 kcal/mol, so the biradicaloid electrons are certainly spin-coupled.

Other “difficult” correlated molecules include Be2 and B2.

References

  1. R.S. Mulliken, "Note on Electronic States of Diatomic Carbon, and the Carbon-Carbon Bond", Physical Review, vol. 56, pp. 778-781, 1939. https://doi.org/10.1103/physrev.56.778

Chemical Bonds at the 21st Century – 2017: the Bond Slam.

Wednesday, August 2nd, 2017

It is always interesting to observe conference experiments taking place. The traditional model involves travelling to a remote venue, staying in a hotel, selecting sessions to attend from a palette of parallel streams and then interweaving chatting to colleagues both old and new over coffee, lunch, dinner or excursions. Sometimes conferences occur in clusters, with satellite meetings breaking out in the vicinity, after a main conference has done the job of attracting delegates to the region. Here I bring to your attention one such experiment, the Bond Slam which is part of a satellite meeting in Aachen to be held September 2-4 2017 on the topic of Chemical Bonds at the 21st Century, following on from the WATOC 2017 congress in Munich Germany a few days earlier.

The Bond Slam involves participants selecting a challenge from 16 topics of current interest and is exposed using a Wiki. A selection of the challenges will be presented in person at the conference, but you don’t have to go to Aachen to contribute virtually to discussion. This sort of format can have novel outcomes.[1] If your interest is piqued by any of the challenges or you cannot resist adding your own, do go visit the site and browse. 

 
 
 

References

  1. P.L. Ayers, R.J. Boyd, P. Bultinck, M. Caffarel, R. Carbó-Dorca, M. Causá, J. Cioslowski, J. Contreras-Garcia, D.L. Cooper, P. Coppens, C. Gatti, S. Grabowsky, P. Lazzeretti, P. Macchi, . Martín Pendás, P.L. Popelier, K. Ruedenberg, H. Rzepa, A. Savin, A. Sax, W.E. Schwarz, S. Shahbazian, B. Silvi, M. Solà, and V. Tsirelson, "Six questions on topology in theoretical chemistry", Computational and Theoretical Chemistry, vol. 1053, pp. 2-16, 2015. https://doi.org/10.1016/j.comptc.2014.09.028

First, hexacoordinate carbon – now pentacoordinate oxygen?

Saturday, March 25th, 2017

The previous post demonstrated the simple iso-electronic progression from six-coordinate carbon to five coordinate nitrogen. Here, a further progression to oxygen is investigated computationally.

The systems are formally constructed from a cyclobutadienyl di-anion and firstly the HO5+ cation, giving a tri-cationic complex. There are no examples of the resulting motif in the Cambridge structure database. A ωB97XD/Def2-TZVPP calculation (DOI: 10.14469/hpc/2350) shows it is again a stable minimum, with a Kekule mode of 1203 cm-1.

A QTAIM  topological analysis of the electron density shows it differs from the nitrogen analogue in now having the ring topological feature for the basal four carbons, which in turn gives rise to a cage critical point (blue dot). The values of the electron density are lower than for N.

The ELF basin analysis shows the C-C bonds are regular single ones (2.01e), whereas the C-O bonds have a slightly greater electron population than the C-N bonds discussed in the previous post.

I suspect the prospects of making a stable tri-cation in such a small molecule are lower than the crystal di-cation achieved with carbon as the apical atom. But the charge can be reduced to a di-cation by replacing the HO5+  above with S-O5+; the animation below showing the Kekule mode (1140 cm-1, DOI: 10.14469/hpc/2356).

And for some (negative) loose ends.

  1. The P equivalent constructed from cyclobutadienyl di-anion and HP4+ is now unremarkably 5-coordinate. But in fact it is not a stable minimum (DOI: 10.14469/hpc/2357), having two negative force constants.
  2. as does the system  from cyclobutadienyl di-anion and O=P4+(DOI: 10.14469/hpc/2358)
  3. and the system from cyclobutadienyl di-anion and HS5+(DOI: 10.14469/hpc/2360).
  4. Transposition of S/O to give O-S5+ likewise (DOI: 10.14469/hpc/2359).

So the family of hyper-coordinate 2nd row main group elements now comprises the experimentally verified C, with N and O now open to such verification.

First, hexacoordinate carbon – now pentacoordinate nitrogen?

Saturday, March 25th, 2017

A few years back I followed a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. That reality was recently confirmed via a crystal structure, DOI:10.5517/CCDC.CSD.CC1M71QM[1]. Here is a similar proposal for penta-coordinate nitrogen.

First, a search of the CSD (Cambridge structure database) for such nitrogen. There are only three hits[2], [3], [4] all of which relate to RN bonded to four borons as part of a boron cage. There are none which relate to RN bonded to four carbon atoms. 

The original argument was based on cyclopentadienyl anion and its symmetric coordination to RC3+ to achieve six coordination for one carbon. Morphing C to the iso-electronic Ngets one to the ligand RN4+ and this can now be coordinated to the di-anion of cyclobutadiene, also iso-electronic in the 6π sense to cyclopentadienyl mono-anion.

The optimised structure of the methylated system (ωB97XD/Def2-TZVPP) as shown below (DOI: 10.14469/hpc/2348) is a true minimum and reveals a 5-coordinate nitrogen. It is the dication of an isomer of pentamethyl pyrrole.

One of the normal modes for this molecule is the so-called Kekule vibration, which elongates two C-C bonds and shortens the other two. The value (1266 cm-1) is typical of aromatic systems.

A QTAIM analysis shows four line (bond) critical points (LCP, magenta) connecting the 4-carbon base of the system and four further LCPs connecting each carbon to the nitrogen. Significantly, the four carbons are not themselves characterised by a ring critical point (RCP, green), these being confined to the rings formed between two carbons and the nitrogen. The value of the electron density ρ(r) at the basal bond is typical of a single bond; the value to the nitrogen indicates the bond has a smaller order.

An ELF (electron localisation function) analysis is similar, showing basal C-C electron basins of 2.12e and C-N basins of 1.25e.

In hunting for examples of hyper-coordination in the second row of the periodic table, the focus has tended largely towards identifying carbon examples. Perhaps that might now right-shift to the adjacent element nitrogen?

References

  1. M. Malischewski, and K. Seppelt, "Crystal Structure Determination of the Pentagonal‐Pyramidal Hexamethylbenzene Dication C<sub>6</sub>(CH<sub>3</sub>)<sub>6</sub><sup>2+</sup>", Angewandte Chemie International Edition, vol. 56, pp. 368-370, 2016. https://doi.org/10.1002/anie.201608795
  2. U. Doerfler, J.D. Kennedy, L. Barton, C.M. Collins, and N.P. Rath, "Polyhedral azadirhodaborane chemistry. Reaction of [{RhCl2(η5-C5Me5) }2] with [EtH2NB8H11NHEt] to give contiguous ten-vertex [1-Et-6,7-(η5-C5Me5)2- closo-6,7,1-Rh2NB7H7 ]", Journal of the Chemical Society, Dalton Transactions, pp. 707-708, 1997. https://doi.org/10.1039/a700132k
  3. L. Schneider, U. Englert, and P. Paetzold, "Die Kristallstruktur von Aza‐<i>closo</i>‐decaboran NB<sub>9</sub>H<sub>10</sub>", Zeitschrift für anorganische und allgemeine Chemie, vol. 620, pp. 1191-1193, 1994. https://doi.org/10.1002/zaac.19946200711
  4. M. Mueller, U. Englert, and P. Paetzold, "X-ray Crystallographic Structure of a 7-Aza-nido-undecaborane Derivative: (NB2tBu3H)NB10H12", Inorganic Chemistry, vol. 34, pp. 5925-5926, 1995. https://doi.org/10.1021/ic00127a034

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

Real hypervalency in a small molecule.

Sunday, February 21st, 2016

Hypervalency is defined as a molecule that contains one or more main group elements formally bearing more than eight  electrons in their  valence shell. One example of a molecule so characterised was CLi6[1] where the description "“carbon can expand its octet of electrons to form this relatively stable molecule“ was used. Yet, in this latter case, the octet expansion is in fact an illusion, as indeed are many examples that are cited. The octet shell remains resolutely un-expanded. Here I will explore the tiny molecule CH3F2- where two extra electrons have been added to fluoromethane.

Two such electrons added to e.g. such a methane derivative can be in principle accommodated in two ways:

  1. The electrons on carbon could expand the octet shell by populating molecular orbitals constructed using 3s or 3p atomic orbitals (AOs) as well as the normal 2s and 2p shells. This is also the normal "explanation" for expanded octets, the assumption being that as one moves down the rows of the periodic table (e.g. P, S, Cl, etc) these shells become energetically more accessible (e.g. the 3d or 4s shell for P, S, Cl etc). In fact, for e.g. PF5, the occupancy of such  "Rydberg" shells is only ~0.2 electrons, not a significant octet expansion.
  2. The electrons can instead or as well as populate the antibonding molecular orbitals (MOs) formed from just the 2s/2p AOs. For a methane derivative, there are four bonding MOs (into which the octet of electrons are placed) and four anti-bonding MOs all constructed from the total of eight AOs. Well known examples of populating antibonding MOs are the series N≡N, O=O (singlet), F-F, Ne…Ne where the additional electrons are added to anti-bonding MOs and have the effect of reducing the bond orders from 3 to 2 to 1 to 0. And of course all core shells contain populated bonding and antibonding pairs.

Here are some ωB97XD/Def2-TZVPPD/scrf=water calculations. All these species are molecules with all-real vibrations, being stable toward dissociation to e.g. CH3 + H or CH3 + F.  A transition state for this latter dissocation with IRC[2] can be characterised. In all cases the energy of the highest occupied MO or NBO is -ve, meaning that the electrons are bound, at least in part due to the solvent field applied.

Molecule Wiberg CH order Wiberg CF order Natural Populations E HONBO, au dataDOI
CH42- 0.773

C:[core]2S(1.98)2p(3.82)3S( 0.15)4d( 0.01)

H:1S( 1.00)

-0.144CH4 [3]
CH3F2- 0.980 1.213

C:[core]2S(1.05)2p( 3.20)3S(1.26)4p( 0.01)4d( 0.01)

H:1S( 0.84)2S( 0.01)2p( 0.02)

F:[core]2S(1.88)2p( 5.61)3S( 0.30)3p( 0.04)3d( 0.01)4p( 0.01)

-0.068
Click for  3D

Click for 3D

[4]
CH2F22- 0.871 0.897

C:[core]2S(1.60)2p( 2.64)3S(0.39)3p( 0.01)4d( 0.01)

H:1S(1.19)2S( 0.06)

F:[core]2S(1.86)2p( 5.52)3S( 0.01)3p( 0.01)4p( 0.01)

-0.281
Click for  3D

Click for 3D

[5]
CF42- 0.801

C:[core]2S(1.94)2p( 1.96)3S( 0.19)3p( 0.04)5d( 0.01)

F:[core]2S(1.89)2p( 5.54)3p( 0.01)3d( 0.02)

 

-0.148CF4 [6]
  1. CH42- shows only small Rydberg occupancy (< 0.2e), but a significantly reduced bond order for the four C-H bonds (each C-H bonding NBO also has some antibonding character for the other three CHs) and hence the molecule is not truly hypervalent.
  2. CH3F2- in contrast shows quite different behavour. The C-H bond order is almost 1 and the C-F bond order is actually >1. Of the two extra electrons, ~1.28 now occupy carbon Rydberg AOs and the fluorine also has significant Rydberg population (~0.36e). So this is a real hypervalent system, in which the total valencies exceed that expected from an octet.
  3. CH2F22- is somewhere inbetween the previous two systems. The carbon has modest Rydberg occupancy (~0.4e) but there is also significant occupation of the antibonding MOs. Both the C-H and C-F bond orders are <1.
  4. CF42- shows a further reduction in the C Rydberg occpancy (<0.2) and the C-F bond order is also reduced. This reduction in bond order is also seen in other so-called hypervalent systems such as PF5.

So of these systems, CH3F2- can be reasonably called hypervalent, whilst the others have much less such character. It does appear that there is a fine balance between placing extra electrons into Rydberg orbitals to expand the "octet" and hence valencies, and placing them in anti-bonding orbitals where the individual valencies are actually reduced. It seems that substituting methane with just one fluorine encourages population of the Rydberg orbitals, but that more fluorines encourage instead population of the antibonding orbitals. What is remarkable is that CH3F2- actually has a (small) barrier to dissociation. The challenge now is to try to design a system which has a significant Rydberg population, a low antibonding population AND is stable to dissociation; this will require some inspiration. So do not hold your breaths!

 

References

  1. H. Kudo, "Observation of hypervalent CLi6 by Knudsen-effusion mass spectrometry", Nature, vol. 355, pp. 432-434, 1992. https://doi.org/10.1038/355432a0
  2. https://doi.org/
  3. H.S. Rzepa, "C 1 H 4 -2", 2016. https://doi.org/10.14469/ch/191837
  4. H.S. Rzepa, "C 1 H 3 F 1 -2", 2016. https://doi.org/10.14469/ch/191919
  5. H.S. Rzepa, "C 1 H 2 F 2 -2", 2016. https://doi.org/10.14469/ch/191918
  6. H.S. Rzepa, "C 1 F 4 -2", 2016. https://doi.org/10.14469/ch/191916