In the news this week is a report of a molecule whose crystal lattice is capable of both storing and releasing large amounts of hydrogen gas at modest pressures and temperatures. Thus “NU-1501-Al” can absorb 14 weight% of hydrogen. To power a low-polluting car with a 500 km range, about 4-5 kg of hydrogen gas would be need to be stored and released safely. The molecule is of interest since it opens a systematic strategy of synthetically driven optimisation towards a viable ultra-porous storage material,[cite]10.1126/science.aaz8881[/cite] much like a lead drug compound can be optimised.
I thought it would be informative to show a 3D interactive model of the crystal lattice here and so I went in search of coordinates. These are indeed available online. This is an example of scientific data Interoperability and Reuse, part of the FAIR data acronym. Before showing the model, I thought it worth briefly describing the procedure for starting with deposited data and converting (interoperating) it to the model here.
- The molecule is a so-called MOF, or Metal-Organic-Framework. The core organic framework in this case is composed of linked tryptycene derivatives. Shown below is the 3D structure of this linker, oriented here to show the three-fold symmetry (actually D3) of the molecule, rather than any attempt to reveal all the atoms without any hidden ones. To see the latter, you are encouraged to click on the diagram and view the molecule as a rotatable model instead. The coordinates below are optimised using molecular mechanics to reveal the role of the linker units.
Click for a rotatable 3D model.
- The data comes in the form of a CIF (crystallographic information) file and needs to be loaded into software that can manipulate such a format. In this case a program called Mercury (from CCDC) is available. Doing so reveals two minor oddities, circled in red below. The phenomenon arises from disorder, or two or more structures each with what is called partial occupancy. In this case, the disorder is largely limited to a p-substituted phenyl spacer linkage, which can adopt one of two rotational positions in the structure. The projection below is now selected to reveal the disorder rather than the symmetry.
- I want to “inter-operate” these coordinates into something that can be modelled and for this, the structure has to be edited to reduce it to a single unambiguous model. My very simple expedient here was simply to remove extraneous disordered atoms entirely; since they are acting as a spacing unit, this is unlikely to change the overall picture.‡ Again, the projection below is selected to show the symmetry present and in particular the hexagonal-like channels that appear in the crystal lattice. To achieve this lattice, the unit cell has to be grown in all three directions using the calculate packing option in the Mercury program.
Click for 3D rotatable model
Clearly, the hexagonal cavities formed can accommodate a large number of hydrogen molecules. As to why, it is no doubt complex, but I cannot help but notice that the surface of the cavity is lined with multiple C-H units from the aryl spacer units pointing inwards. Given that hydrogen is a very good inducer of dispersion attractions, it would be interesting indeed to see whether the very large number of H…H2 dispersion attractions possible inside the cavity of this species might at least in part be responsible for the ability of this framework to accommodate hydrogen (or methane) gas.[cite]10.1039/C6SC02727J[/cite] It would be good to have an estimate of the dispersion energy term for NU-1501-Al and related species and the contribution of this term to the overall thermodynamics of the system. By the same token, replacing the four aryl C-H units with C-F units (a weaker dispersion attractor, think non-stick teflon) should reduce the ability to absorb hydrogen if dispersion is indeed important.
‡On the other hand, if the orientation of the aryl C-H groups is important in terms of dispersion attractons, perhaps these groups are actually critical to the effect.
I find that when I scroll the page using two fingers on my Mac touchpad that it will annoyingly resize the image when the pointer gets to the embedded image. Shrink it to a pint scrolling down, and vv going up. Not just with jsmol, as here, but often with things like Google maps too. But not on all pages with such scalable images, which suggests that there is a setting somewhere for authors to prevent this behaviour.
Maybe it’s an Apple laptop/touchpad thing and as such isn’t often reported??