This is a continuation of the discussion started on Steve Bachrach’s blog about a molecule with a very short H…H interaction involving two Si-H groups with enforced proximity. It had been inferred from the X-ray structure[1] that the H…H distance was in the region of 1.50Å. It’s that cis-butene all over again! So is that H…H region a bond? Is it attractive or repulsive? Go read Steve’s blog first.
Next, in the previous post, I had blogged about assigning a publication doi to a procedure or tool. So Steve’s post provided a good opportunity to show how this might work. This is the tool doi: 10.6084/m9.figshare.811862 Using it, and another doi, this time data: 10.6084/m9.figshare.812621 we can create a new data set, visualised below.‡ This is the NCI (non-covalent-interaction)[2] isosurface of the reduced density gradient, and colour coded according to (λ2)ρ, the eigenvalue of the density Hessian, to indicate attraction or repulsion. You should know that according to this scheme, blue is strongly attractive (it is normally seen for example for strong hydrogen bonds). You can see the blue region in-between the H…H region. So a strong (di)hydrogen bond then!
Click for 3D.
Well, interesting, and this needs to be looked into further. For example, it might in fact be an anomalous result since the H…H region may in fact have charge-shift character,[3] which can change the characteristics of the density Hessian (and its Laplacian).
One more property, the NBO (natural bond orbitals) for this region. Can one tell if H…H is bonding? It might seem so. Finally, the Wiberg bond index for the H…H region is 0.027, very slightly bonding.
Click for 3D.
Click for 3D.
I should conclude by stating that whilst the initial discussion of this molecule took the form of comments on Steve’s blog, the nature of the Word press system used there (and here) does not allow commentators to insert rotatable models into comments. So that discussion is continued here in order to achieve that effect.‡
‡ And yet another data-doi could be created showing the interactive display, and this could be transcluded back into Steve’s blog to continue the to and fro.
Postscript: I have added the QTAIM analysis that first appeared on Steve’s blog. The red arrow points to the H…H bcp. The blue arrow points to one of the other (three in all) bcps, all of which are very close to a ring critical point, and hence should be regarded as unstable and prone to annihilation.
Click for 3D.
The B3LYP+D3/TZVP calculated Si-H vibrations are shown below. The VCD spectrum[4] is shown below it.
Click for animation
Postscript 2. The Si-H vibration is reported as 2325 cm-1 (with weak bands at ~ 2360-2380), but in footnote 7 of the original report[1] the authors do note that there should be two Si-H bands. The calculation shown above suggests two values, 2406 (intensity 37) and 2460, intensity 10).
The 1H NMR spectrum of the two Si-H bands has two singlets which are reported (but not discussed in the text anywhere) as 8.23 and 8.56 ppm (Δδ 0.33ppm, CDCl3); B3LYP+D3/TZVP calculation[5] predicts 8.79 and 9.40 (Δδ 0.61 ppm). It is possible however these shifts are perturbed by spin-orbit coupling from the silicon[6]. The diastereotopic methylene groups are reported as 4.10 and 4.83, calc 3.95 and 5.03 ppm, which is a reasonable match, and gives confidence to the theoretical prediction.
The 29Si NMR is reported as -32 and -40 ppm, calculated -31.6 (for the Si-H associated with bridging S) and -39.9 (for the Si associated with bridging C) ppm, which matches very well.
The reported 1H NMR spectrum appears to show 29Si satellites but their values are not reported numerically in the article. In Ph3Si-H, this coupling is known to be ~±205 Hz. The 29Si-1H couplings are calculated for the compound above as -191 (for the -31.6 peak) and -166 Hz (for the -39.9 peak), this latter being notably lower than the former. The 29Si-29Si coupling is 10 Hz. Most interestingly, the 0JHH coupling (i.e. through space) is predicted as +5.4 Hz; there is no sign of such a coupling for the two singlets reported at 8.23 and 8.56 ppm. This last observation may be of significance in terms of whether the axis along the four atoms Si-H-H-Si is indeed linear, or whether it is bent (enabling the two hydrogens to avoid close contact).
This problem is not yet closed!
In the mid to late 1990s as the Web developed, it was becoming more obvious…
I have written a few times about the so-called "anomeric effect", which relates to stereoelectronic…
The recent release of the DataCite Data Citation corpus, which has the stated aim of…
Following on from my template exploration of the Wilkinson hydrogenation catalyst, I now repeat this…
In the late 1980s, as I recollected here the equipment needed for real time molecular…
On 24th January 1984, the Macintosh computer was released, as all the media are informing…
View Comments
The spin-spin coupling constants computed and reported in the post above were done at the B3LYP/TZVP level. They are however known to be sensitive to basis set. A procedure that decontracts the basis to correct for this effect can be applied (doi: 10.1021/ct600110u, implemented in Gaussian as NMR(spinspin,mixed) ). This results in the following predicted couplings;
29Si-H, -245 and -210 Hz; 29Si-29Si, +11.1, 1H-1H +6.2 Hz.
This calculation can be found at doi: n8r.
Bob Pascal has kindly sent me the measured J(SiH) couplings, as ±233 (δ8.57) and ±206 Hz (δ 8.24). These compare with calculated values of -245 and -210 Hz respectively.
Bob has sent me some more data, this time on an analogue (below) where a P replaces one of the S-H groups, and suggested I post them here to continue the discussions. These results come from an article about to be published in Tetrahedron (doi: tba).
In order to further calibrate the NMR predictions, this system has the following measured values: δ29Si -35.8, 31P -48.9, and 1H 9.31 ppm. J(SiH) = ±248 Hz, J(SiP) = ±76 Hz, and J(PH) = ±25 Hz
The calculated values are: δ29Si -34.9, 31P -42.7, and 1H 10.1 ppm. J(SiH) = -262 Hz, J(SiP) = -87 Hz, and J(PH) = -29 Hz.
The most interesting of these is the through-space PH coupling. In truth, I have no idea if this is unusually large or not; does anyone know?
Computation allows one to ask what if. So, "what if one replaced the -S- bridge in the Si-H...H-Si system with an oxygen bridge"?
The NMR reveals a through-space H-H coupling of +8.0Hz, and a H-H distance of 1.47Å, which would be another record. Whether this system can be made synthetically is another question however.
The IR has two Si-H stretches of 2452 and 2523 cm-1 which also reveals a stable minimum with no distortive imaginary modes.
Roald Hoffmann has pointed out to me modelling of SiH4 at high pressures. It takes 150 GPa (~1.5 million atmospheres) to shrink the H...H distance to 1.5Å or less. Since this around the value reported by Pascal et al, this implies the internal compression is equivalent to ~1.5 million atmospheres. Pretty impressive!
“Any ideas for a compound with an even shorter non-bonded H…H distance?”
Yes, there is! See my joint paper with Dr. Firouzi just posted to arxiv: http://arxiv.org/abs/1310.5375 for examples of shorter non-bonded H...H distances. we have reach to distances as short as 1.38 Å however, I think even shorter distances are also possible to be realized at least computationally.
In response to the previous comment, I show a diagram of one of the species suggested there. Whether this system could be synthesized is an interesting question; it does look very highly strained. I would also observe that the C-H-H-C alignment below is very non-linear, whereas the Si-H-H-Si is completely linear.
I also calculated the H…H through space NMR coupling, and this comes out as +4.6 Hz, lower than the Si-H…H-Si coupling of ~6Hz (but is this because it is non-linear?). This might also suggest that the predicted magnitude of the Si-H…H-Si coupling is associated in part at least with the nature of the Si atom (and any spin-orbit effects that might accrue for this element, but not for C). Clearly, a high level calculation, which includes such corrections, does seem a desirable objective to clarify this point.
"Whether this system could be synthesized is an interesting question; it does look very highly strained."
Indeed. I think the strain energy (MM methods) or alternatively the energy of formation (QM methods) must be calculated to see whether there is any chance for this and other proposed systems to be synthesized although the "kinetic stability" is also an important issue. These are rigid hydrocarbons so there is no problem with conformational variations however, the case of severe deformation can not be excluded and this may ruin the kinetic stability. For the case of B6C(-2) some years ago I have done such project (J. Phys. Chem. A, 2008, 112 (41), pp 10365–10377) (check the DOI: 10.1021/jp806874u) and considered all deformation pathways so I know it is simple to say but hard to do such calculations! To realize linear CH...HC form, I think "3D" hydrocarbon skeletons must be designed (probably Pascal's own design is somehow an example for using 3D structures) to put "pressure" from below and above on CH...HC making it impossible for severe non-linear deformations toward a less crowded corner.
It is strange that these and similar problems have not yet been considered computationally...
The molecule above might be susceptible to homolytic cleavage, and I note that one can try to estimate the energies for this sort of process according to the procedures outlined at 10.1021/jz401578h for in effect the dissociation of F3SSF, by systematically testing each bond.
thoughtful idea...
Regarding the role of linear vs. non-linear CH...HC arrangements, though not for ultrashort H...H contacts, there are useful discussions at 10.1021/ct400070j and 10.1038/nchem.1004
Regarding the "3D" structures that may be used to force certain arrangements of atoms I found these two works from Leo Radom in my files on exotic hydrocarbons: Angew. chem. Int. Ed. 38, 2876 (1999) and Pure. Appl. chem. 70, 1977 (1998). Although they are not directly relevant to above discussions but demonstrate how design in "3D" may be used to achieve a certain configuration of atoms.