August 29th, 2017
The triennial conference is this year located in Munich. With 1500 participants and six parallel sessions, this report can give only a flavour of proceedings.
- Edward Valeev talked about the scaling problem in coupled cluster theories, the so-called gold standard for computing the energy and properties of small molecules. The problem is that the number of basis functions N describing the atomic basis set for the atoms scales from between N6 to N10 in terms of computer time, with similar behaviour for the memory required for the calculation. He described methods based on natural pair orbitals and localisation schemes which can achieve linear scaling, ie N1 for the energy, quite a break through! Using reasonable basis sets, CCSD(T)-like energies for molecules with 100s of atoms were reported. During the Q&A time afterwards (the tight schedules associated with so many speakers means questions are often limited to 1-2, with very short answers) a question was posed about the prospects for first and second derivatives for the method. This means that e.g. reaction mechanisms can then be probed with unprecedented energetic accuracy. The answer was non-committal, but if these derivatives do arrive, it will revolutionise our ability to understand mechanisms.
- Which brings me nicely to Jeremy Harvey, who talked about calculating accurate overall rate constants for complex mechanistic cycles. The rate equations are solved for the steady state condition and include concentrations of all species and the energies are obtained using CCSD(T)-F12 theory (a modification which allows better basis set scaling without increased computation time) as single point geometries. He described an example where the barrier associated with a postulated mechanism was about 6 kcal/mol higher than derived from the observed rate. This was sufficient to induce them to explore alternative mechanisms, which were indeed located with an appropriately lower barrier. I have used the value of ~10 kcal/mol as my mechanistic test on this blog, and it’s really nice to see this value being reduced further.
- Yet again this theme emerged with Yitzhak Apeloig, who asked about the mechanism for C=Si bond rotations in substituted systems recently made in his group. The energy of this rotation is low enough to be observed in NMR spectra. But when the energy of C=Si bond rotation is computed it comes out about 10 kcal/mol too high. Again alternative mechanisms were explored and it turns out that a 1,2 migration from R2C=SiR2 to form a carbylidene species, R-C-SiR3, rotation and then 1,2 again to reformulate the R2C=SiR2 system came up with the goods.
- Peter Scheiner talked about how attractions between molecules can be induced by dispersion. He described how Ph3C-CPh3 is an unknown molecule (dissociating into Ph3P• radicals) but when 4,6-di-tert-butyl groups are placed on all the phenyl rings, the dispersion attractions between them can account for ~60 kcal/mol (!), more than enough to stabilise the system. I have already described some of this work in a post here. The prospects are very exciting for more dispersion-stabilised molecules to emerge. During Q&A, a question was posed about what other atom pairs other than H…H might be brought into ultra-short contact by these attractive dispersion forces; we may expect further examples to emerge in the near future.
- Ken Houk gave a fascinating glimpse into the post-transition state world of reaction dynamics, as applied to Diels Alder cycloadditions and Cope rearrangements. The reactions are characterised by the residency times of the dynamic trajectories in the region of the transition state as short (~4 fs), medium (20-40fs) and long (80+fs), these times mapping on to what we used to call “synchronous”, “asynchronous” and “stepwise”. A good example is the so-called bis-pericyclic reaction of cyclopentadiene where the trajectories pass through a transition state but then bifurcate into two (in this case) equivalent pathways. He discussed other examples where the trajectories follow either a 2+4 cycloaddition pathway or a 4+6 alternative pathway and how the number of trajectories for each can be influenced by either solvent (water) or an enzyme. Ken described several 20-40fs trajectories as corresponding to “dynamic stepwise” reactions, which during Q&A was suggested are equivalent to the term “hidden intermediate” pathways coined by Dieter Cremer and as revealed in many posts here from the intrinsic reaction coordinates or IRCs. This is a clear growth area and expect many more examples of reaction dynamics to be applied to many exciting systems in the future.
- Leo Radom talked about very simple molecules, H3CX and the effects on the bond dissociation energy (BDE) of the C-H bonds if the group X is either strongly or weakly protonated (the latter via a hydrogen bond), or deprotonated (again strongly or weakly via a hydrogen bond from hydroxide anion). This is important in several enzymic pathways, where the CH bond might be activated in a similar manner by the enzyme. He also talked about similar effects on the ionisation potential. I noticed a connection between this theme and what might be called the electron affinity of H3CX. If you want to see what the connection is, go visit the Aachen bond Slam, about which I have previously blogged!
I will stop with an observation that all the notes above were taken in real-time during the talks, which all emerged as Powerpoint slides, having an average residency time on the screen of perhaps 1-2 minutes each. References were invariably given as full journal citations (authors, journal, year, volume, pages) rather than as DOIs, and given the time constraints I did not try to capture them. Hence the lack of citations above to the presenters’ work. The slide displays are traditionally not made available to audiences‡ and photography of the screen or recording is considered very bad form. Conferences are not really about FAIR data, which I have described often on this blog.
I hope these six examples give one flavour of what is happening at WATOC 2017. If another interesting collection emerges, I may describe it here.
‡But see e.g. doi: b9r9 for an Aachen talk.
Tags: bond dissociation energy, City: Aachen, City: Munich, Dieter Cremer, Edward Valeev, energy, Flavour, Jeremy Harvey, Ken Houk, Leo Radom, Peter Scheiner, Physics, Proceedings, Quark matter, Standard Model, Yitzhak Apeloig
Posted in Interesting chemistry, WATOC reports | No Comments »
August 12th, 2017
At the moment, the bond slam is something of a home from home for this blog and since much of my activity is happening there rather than here, I thought I might give you pointers to some of the topics, which are evolving, so to speak, before our very eyes.
- The topic of agostic interactions (or perhaps bonds) was seeded by a graduate student (with some encouragement perhaps from his supervisor). It is a different kind of hydrogen bond, one specifically involving a metal. As per many types of bond, it has its controversies! Thus is it useful to fragment this into true agostic interactions and into those which are merely anagostic? How should the calculated wavefunction for a molecule exhibiting the effect be analysed? Geometries, normal mode frequencies, electron density shifts, QTAIM, NCI, NBO, ELF are all discussed, thus far with much apparent agreement! I have contributed some crystal structure searches, such as the one below. If you want to understand what these acronyms all mean, go visit the topic, and perchance even contribute!
- Readers of this blog might have noticed the topic of hypervalence has occasionally appeared, sometimes coupled with hypercoordination. Often these two terms are loosely interchanged in their meaning and it is certainly (I believe) often taught even more loosely in undergraduate lectures. For my take on the topic, go visit the slam, where some examples of what I choose to call true hypervalence are suggested. It is not as common as you might think!
- Molecular electrides make an appearance, again a topic I have occasionally covered on this blog.
- Penta and hexa-coordinate carbon (not to be confused, but probably it will be, with penta and hexavalent carbon) make separate appearances, with some new suggestions for hitherto undiscovered analogues for other elements.
- But the most unusual and original suggestion is that we consider the properties of Positronium Hydride or PsH. One for the physicists to detect I fancy!
There are still around three weeks to go before the live debate in front of an audience, so check regularly to see what new insights might have been added.
Tags: Interesting chemistry
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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
- 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
Tags: Interesting chemistry
Posted in Bond slam, Interesting chemistry | 3 Comments »
July 24th, 2017
Bees are having a tough time around the world. Oddly, they are surviving very well in cities. One reason are the wild flower meadows in London and for some summer relief I thought I would tell you the story of the one shown below.
We live in west London, in an area that was farmland as recently as the 1930s and used to produce vegetables and milk for the population of London. When the London underground (the “tube”) was extended into this rural west, housing sprung up around the central and metropolitan lines (Metroland). In our case, the large meadows adjacent to the new housing were left undeveloped due to their propensity to become waterlogged and flooded from the nearby river Brent. Flood prevention schemes have now made such flooding largely a thing of the past and part of the meadows have been turned into a golf course. But the area that you see above is largely left to nature and in the normal course of events the grasses grow copiously and cause the local population to suffer mightily from hay fever between June-August.
Not this year, when a tractor from the local council (Ealing) turned up in March and ploughed the grassy area up! For two months it lay fallow because there was almost no rain in May or June, but after several decent showers the area started to bloom and we all realized that the tractor must also have sown wild flower seeds. Its been a riot of colour for more than a month now and looks likely to continue for a little while yet. The bees love it (it’s not been such a good year for butterflies however). So do the human residents; you can see our house in the background! On a number of occasions now, contemplating the start of a new day, I have wandered out into the meadow, frankly with all thoughts of writing a blog abandoned. Except this one, since I did feel like sharing our pleasure. I cannot share the scent of the flowers however, which is also pretty heady. I should perhaps also mention that rather to the left of the photo above is the river Brent and along its route grows wild mustard in spring and many a bramble bearing luscious fruits in July. Foraging for these is another delight!
Update on 4th August, 2017. Perivale Park, UB6 9BG
Update on 20th August, 2017. Perivale Park, UB6 9BG
Update on 6th September, 2017. Perivale Park, UB6 9BG
Update on 17th August, 2017. Cayton Green Park. UB6 8BJ.
Update on 11th August, 2017. King George’s Playing Fields, UB1 2QA
Update on 11th August, 2017. Jubilee Park, UB1 2TJ
Tags: Animal dance, Bee, Behavior, Flower, George, King, Meadow, Person Career, Person Location, Plant reproduction, Pollination, Reproduction, river Brent
Posted in General | 6 Comments »
July 21st, 2017
There is much focus at the moment on how to ensure experimental replicability in e.g. the molecular sciences. An important aspect of that is having access to FAIR data; data which is findable, accessible, inter-operable and re-usable. One of the “gold standards” in chemistry is the data associated with crystal structures. Here I take an inside peek into the standard file-type for carrying crystal structure data, the CIF file (the Crystallographic Information File).
CIF is a tightly managed format, with utility tools such as checkCIF to validate the files and check for errors. It is also what is called a processed data format, created from structural analysis of the raw image data that emerges from a diffractometer, and is therefore what might be described as a lossy format. Discussing these aspects with our crystallographer here (thanks Andrew!), I began to realise that there are at least three distinctly different versions of a CIF file, each carrying a different degree of data loss.
I am going to take as my illustration of this structure[1] known by three different identifiers; AZUJOW, CCDC 1406199 or DOI: 10.5517/ccdc.csd.cc1j6888
- The CIF originates with the authors and this version is 449KB in size. I have deposited it and the other two at DOI: 10.14469/hpc/2752 for you to inspect and compare them. This file is relatively large since it contains the so-called structure factors or hkl information, a snippet of which looks like:
_shelx_hkl_file
;
0 0 1 108882. 1066.19 2
0 0 2 320.055 130.609 2
0 0 3 18538.0 806.608 2
0 0 4 173192. 2808.03 2
- This information is removed using a utility known as shredcif to produce a second version, known as the name_x.cif version and reducing the size to 27KB. This retains information about properties such as thermal ellipsoids and bond length and angle information but loses the hkl information.
- After the CIF is submitted to CSD, it emerges as AZUJOW.cif, which is now just 7KB in size and is now missing the bond lengths and angles etc.
The original raw image data for this structure is not publicly available, but you can see a set of structures for which it IS available at DOI:10.14469/hpc/2297 (published as [2] and where the file sizes are typically 200-600 MB (they can get much larger).
So a CIF can vary in data content between 7- 449KB, and the original “raw” data can be ten thousand times larger than this! To acquire all the flavours, you have to access both the CSD and contact the original authors (unless of course the latter have deposited their versions in an open data repository, as above).
Fortunately for most chemical applications, even the “lossiest” of the CIF formats is more than adequate. But for the gold standard in chemical data, you should be aware that you may still be losing access to a lot of original data in the CIF formats and of course to all of the raw diffractometer data. I think it fair to say however that there is now momentum to increasingly retain as much of this data as is possible for posterity.
References
- A. Toscani, K.A. Jantan, J.B. Hena, J.A. Robson, E.J. Parmenter, V. Fiorini, A.J.P. White, S. Stagni, and J.D.E.T. Wilton-Ely, "The stepwise generation of multimetallic complexes based on a vinylbipyridine linkage and their photophysical properties", Dalton Transactions, vol. 46, pp. 5558-5570, 2017. https://doi.org/10.1039/c6dt03810g
- J. Almond-Thynne, A.J.P. White, A. Polyzos, H.S. Rzepa, P.J. Parsons, and A.G.M. Barrett, "Synthesis and Reactions of Benzannulated Spiroaminals: Tetrahydrospirobiquinolines", ACS Omega, vol. 2, pp. 3241-3249, 2017. https://doi.org/10.1021/acsomega.7b00482
Tags: Chemical IT
Posted in Chemical IT | 7 Comments »
July 18th, 2017
The effects of loading up lots of dispersion attractions (between t-butyl groups) into a compact molecule has the interesting consequence of allowing two “non-bonded” hydrogen atoms to approach to ~1.5Å of each other, thus creating the appearance of a “bond” where one normally would not be found. Can such an effect be injected into other combinations of two atoms, say H and F? Here I briefly explore this notion.
The system is a slightly modified version of the one[1] already studied; R3C-F…H-CR3 (R=3,5-bis-t-butylphenyl), and a B3LYP+D3BJ/6-311G(d,p) calculation‡ (with C3-symmetry imposed) shows (DOI: 10.14469/hpc/2734) the following, with the key atom pair distances shown below. Note the abnormally short F…H distance, and the relatively long C-F one.
Note the casual phrase “C3-symmetry imposed”. This is a little “shortcut” one can try to use to shorten the calculation time. I should explain that on our computer system here, we are allowed a maximum of 72 hours per calculation. I already suspected that without the use of such symmetry the calculation would take longer and so used symmetry to “fit the calculation in” to this time slot. In the event it took 55 hours. There is a simple test however to see if this shortcut is justified; does the resulting molecule have 3N-6 real normal vibrational modes (i.e. ones with +ve force constants)? In fact this system fails this test; two of these modes have small negative force constants, corresponding to ν -11 cm-1. You might think this is small enough to perhaps attribute to e.g. the use of too-small a basis set or some other computational imperfection. Actually, although -11 cm-1 is numerically small, the mass-weighting associated with the vibration is in effect the entire system (below) and hence this mode is indeed significant.
So time to release the symmetry and when one does this an entirely different geometry emerges (DOI: 10.14469/hpc/2736) for which now all the 3N-6 normal modes have +ve force constants.
The “non-bonded” F…H interaction is now considerably longer, although still ~0.5Å shorter than the sum of the van der Waals radii (~2.65Å). This F…H non-bonded distance shows up as below in the Cambridge structure database (CSD) distribution. This suggests the shortest interaction is indeed ~2.1Å. The string of isolated examples with shorter distances down to < 1Å are very likely all crystallographic artefacts or errors.
So we may conclude that using the same system that was so successfully used to demonstrate the dispersion-induced ultra-short H…H distance cannot be modified to produce any such extreme effects in the F…H pair. Perhaps indeed “dispersion bonds” will always be limited to H…H pairs.
‡ When this method is used for the original H…H system, it yields a H…H distance of 1.529Å for which all the normal vibrational modes are real; DOI: 10.14469/hpc/2739).
References
- 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
Tags: Interesting chemistry
Posted in Interesting chemistry | 3 Comments »
June 29th, 2017
In the previous post, I noted the crystallographic detection of an unusually short non-bonded H…H contact of ~1.5Å, some 0.9Å shorter than twice the van der Waals radius of hydrogen (1.2Å, although some sources quote 1.1Å which would make the contraction ~0.7Å). This was attributed to dispersion attractions accumulating in the rest of the molecule. I asked myself what the potential might be for other elements to reveal significantly contracted non-bonded distances as a result of dispersive attractions.
Here is a simple search of the CSD (Cambridge structure database, query DOI: 10.14469/hpc/2700) for the monovalent halogens as in C-X. The other constraints are R<0.05, no errors, no disorder, normalised hydrogen positions and a non-bonded intermolecular contacts ≥0.4Å shorter than the sum of the van der Waals radii (a recent compendium of atomic values is available here[1]). I should state at the outset that this sort of search for non-bonded contacts is quite effective at revealing errors in the crystallographic determination, despite the search request that there be none. None, that is, that have been identified; there are many that have not been! So this survey only aims to tease out any broad trends, rather than a specific focus on individual systems.
We see from these results that the number of short H…H contacts far exceeds those found for the halogen series.‡ Clearly whilst the electron density surrounding H is low, that for the halogens is far higher and hence that electron repulsions are going to be far greater. The effect is attenuated if one partner is H itself, with van der Waals contractions in-between those for X…X and H…H contacts.
This brief survey suggests that H…H distances are by far the best for probing close contacts brought about by dispersion attractions. Perhaps the next element to focus on for such effects might be chlorine rather than fluorine. For example, see DOI: 10.5517/cczjyhx, being Ph3C-Cl…Cl-CPh3 where the Cl…Cl distance is contracted by ~0.3Å. What would happen if the Ph groups were adorned with t-butyl groups to increase the dispersion attractions?
‡ It might of course also mean that the van der Waals radius for H is set too high.
References
- S. Alvarez, "A cartography of the van der Waals territories", Dalton Transactions, vol. 42, pp. 8617, 2013. https://doi.org/10.1039/c3dt50599e
Posted in crystal_structure_mining | 8 Comments »
June 29th, 2017
In the previous post, I noted the crystallographic detection of an unusually short non-bonded H…H contact of ~1.5Å, some 0.9Å shorter than twice the van der Waals radius of hydrogen (1.2Å, although some sources quote 1.1Å which would make the contraction ~0.7Å). This was attributed to dispersion attractions accumulating in the rest of the molecule. I asked myself what the potential might be for other elements to reveal significantly contracted non-bonded distances as a result of dispersive attractions.
Here is a simple search of the CSD (Cambridge structure database, query DOI: 10.14469/hpc/2700) for the monovalent halogens as in C-X. The other constraints are R<0.05, no errors, no disorder, normalised hydrogen positions and a non-bonded intermolecular contacts ≥0.4Å shorter than the sum of the van der Waals radii (a recent compendium of atomic values is available here[1]). I should state at the outset that this sort of search for non-bonded contacts is quite effective at revealing errors in the crystallographic determination, despite the search request that there be none. None, that is, that have been identified; there are many that have not been! So this survey only aims to tease out any broad trends, rather than a specific focus on individual systems.
We see from these results that the number of short H…H contacts far exceeds those found for the halogen series.‡ Clearly whilst the electron density surrounding H is low, that for the halogens is far higher and hence that electron repulsions are going to be far greater. The effect is attenuated if one partner is H itself, with van der Waals contractions in-between those for X…X and H…H contacts.
This brief survey suggests that H…H distances are by far the best for probing close contacts brought about by dispersion attractions. Perhaps the next element to focus on for such effects might be chlorine rather than fluorine. For example, see DOI: 10.5517/cczjyhx, being Ph3C-Cl…Cl-CPh3 where the Cl…Cl distance is contracted by ~0.3Å. What would happen if the Ph groups were adorned with t-butyl groups to increase the dispersion attractions?
‡ It might of course also mean that the van der Waals radius for H is set too high.
References
- S. Alvarez, "A cartography of the van der Waals territories", Dalton Transactions, vol. 42, pp. 8617, 2013. https://doi.org/10.1039/c3dt50599e
Posted in crystal_structure_mining | 8 Comments »
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
- 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
- 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
- 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
Tags: 10.1021, Blog, chemical shift, chemical shift difference, chemical shifts, gas phase, Oxygen, Steve Bachrach
Posted in Interesting chemistry | 3 Comments »
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
- 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
- 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
- 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
Tags: 10.1021, Blog, chemical shift, chemical shift difference, chemical shifts, gas phase, Oxygen, Steve Bachrach
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