supramolecular chemistry

Under pressure, from chaos to order.

~ moleculardreams ~ 4 Comments

What happens to a liquid mixture when it is driven by pressure into an initially empty container? What if the container has an ordered pattern of molecular-sized pores? To answer this question, we prepared a sort of good vodka drink – three parts water, and one ethanol – and we injected it into the pores of an hydrophobic container – the zeolite ferrierite. As hydrophobic materials  don’t like water and don’t care about drinks, we had to be very drastic:  we used a diamond anvil cell. In this apparatus, the sample – the empty container and the mixture, in our case –  is compressed between the tips of two opposing diamonds and experiences huge pressures – about 10.000 times the normal atmospheric pressure.  At these conditions,  matter is subjected to unimaginable forces, comparable to internal atomic forces: this means that strange, unexpected phenomena could show up. Now, let’s combine the power of high-pressures  with the ordering effect of the pore matrix and see what happens to our mixture.

Just to start with, the water-ethanol mixture – the pressure-transmitting medium – enters the pores of the matrix.  But how do the molecules occupy the pores? You don’t need to be a chemist to know how it is difficult to separate alcohol from water. This is a critical issue also for sustainable processes – such as the production of biofuels.

Thanks to high pressure and to the porous matrix – and with the help of computational modeling – here we obtained the separation of ethanol from water, and the formation of a beautiful pattern of clusters.  The clusters – rows of ethanol dimers, and square water tetramers – occupy different regions of the host matrix and alternate like tiles forming a nice molecular mosaic – a “two-dimensional architecture” – inside the porous host.  What’s really exciting about it is that the ordered pattern, created by high pressure, also remained stable by bringing the material back to atmospheric pressure.  This means that using high pressures and porous hosts, we can create new materials, which are stable at normal conditions, and could potentially be exploited in applications.

The metamorphosis of the initial water-ethanol solution into a beautiful two-dimensional pattern remains somewhat mysterious. More in general, how organization arises from chaos is still one big question in science.  However, our molecular dynamics simulations show that water molecules, already inside the pores, can spontaneously self-organize in square tetramers:

The final result, is the formation of the stable two-dimensional architecture of water and ethanol clusters. As the movie shows, the molecules move, but the clusters do not break apart. – even upon returning to room pressure.

Perspectives

Disclosing the way in which molecules and nanoparticles assemble at high pressure conditions, under the guidance of a suitable matrix would be a great and intriguing challenge for future studies. Another one would be the actual production of technologically relevant materials through the combined use of pressures and suitable porous matrices.  These goals could be achieved only through a close collaboration between experiment and theory – a synergy which has been at the very origin of the present work.

In a wider perspective, understanding the behavior of matter at high pressures is  of central relevance in science, as explained in this excellent introductory feature article.  Pressure effects are ubiquitous, in chemistry, physics, earth and planetary sciences, as well as in many industrial processes and technological applications.  High-pressure conditions are also hypothesized to explain the origin of complex chemistry and life. The study of this exotic regime, so different from our everyday-life, may reveal plenty of phenomena which would be hard to imagine based on our experience.

Reference: Irreversible Conversion of a Water–Ethanol Solution into an Organized Two-Dimensional Network of Alternating Supramolecular Units in a Hydrophobic Zeolite under Pressure, by Rossella Arletti, Ettore Fois, Lara Gigli,  Giovanna Vezzalini, Simona Quartieri, and myself. Angewandte Chemie 2017 – DOI:  http://dx.doi.org/10.1002/anie.201610949
http://dx.doi.org/10.1002/ange.201610949

Special thanks to Andrea Stangoni (@andrea_stangoni), author of the cover artwork.  His image summarizes the ideas of our work much more beautifully than my blog post!

ange201700219-toc-0001anie201700219-toc-0001-m

And, of course, big thanks to Angewandte too! 🙂

Here are the official versions of the cover:

http://dx.doi.org/10.1002/anie.201700219
http://dx.doi.org/10.1002/ange.201700219

Hope you enjoyed the movies, both (equilibration and final) available at figshare.

Update:  the green open access (accepted article) version of this paper is now freely downloadable from the figshare repository.

How large molecules cross narrow pore entrances

~ moleculardreams ~ 4 Comments

How can a snake swallow a mouse bigger than its mouth?

Weird as it seems, questions like this emerge very often at the molecular scale. For example, we can fill porous materials with molecules larger than the diameter of the pores: in this way, we may obtain devices for energy and health applications. What makes this useful process possible? Flexibility is the key: both the porous host (the “snake”) and the molecule (the “mouse”) must deform for the process to occur. But here, contrary to the mouse-snake case, cooperation between the two partners is needed.

We captured the passage of a bulky molecule through the very narrow opening of one of these pores. We did this by computer simulations, because it is very hard to get such information experimentally. To get an idea of what we found, you don’t even need to read the paper – and i’m not kidding. Just look at the movie below!

What we’ve seen first, is that the pore is slightly larger at its entrance. This surely helps the molecule to go in.

Second: contrary to the mouse, which would escape the snake as fast as it could, the molecule is indeed “magically” drawn to the pore entrance – by electrostatic forces.

“So what?” – you may say.

Keep in mind that the molecule is still larger than the pore opening. No kind of “fatal attraction” could do the trick, in a world of rigid bodies.

We’ve found that the molecule can pass through the opening and slip inside the pore only because it’s flexible, and its motion is “in tune” with the vibrations of the porous matrix. All this factors cope to make the entrance process more favorable than the exit process – that’s why the molecule gets finally swallowed by the pore, and remains trapped inside the material.

For me, it was very nice to see how bulky molecules manage to pass through narrow openings and travel inside a porous material. But finding out the reason why they stay inside was, probably, even more exciting:  because it explains how materials of this kind can form and remain stable. Which is exactly one of the things you may need, in the quest of  easier and smarter ways to produce better materials.

newchannel
Chem. Commun., 2016, DOI: 10.1039/C6CC05303C
Acknowledgments
 As we have to give credit where credit is due, i must confess that i borrowed the mouse-and-snake idea used in this post. But you’ll never know from whom. Me neither: (s)he was an anonymous referee of the paper. I am very grateful to this person: i can hardly imagine a nicest way to sketch our work.
Update: 
Many thanks, of course, also to ChemComm for the cover!
cc_cover

disassembling molecular machines

~ moleculardreams ~ Leave a comment

To understand how a motor works you have to know how it is put together and how it can be disassembled. This is true at the molecular level as well. Amazingly complex molecular motors and machines are fabricated everyday,  but how do they break down into their constituent pieces? Attracted by this question, we modeled two such species – called ‘rotaxanes’ –  and made them break apart.
Typically, rotaxanes are made by two molecules: a ring-shaped one,  the “wheel”, and an approximately linear one, the “axle”. What is great about them, is that you can modify the interactions between the ring and the axle by using an external signal. Which means that you can control the movements of these components through light, for example.

anello
A ring (R)
axe_trans
An axle (EE)
axe_cis
Another axle (ZZ)

Using the three components shown above – one ring and two axles – you can build two different rotaxanes: R-EE, and R-ZZ.  Both disassemble – or ‘dethread’ – when the axle exits from the ring.  This process occurs differently for the two species: While the EE-one (video 1)  dethreads in one single step:

the dethreading of the ZZ-axle (video 2) passes through an intermediate and a transition state:

Analyzing the two simulations, we identified the interactions between the molecular components which control the process at the molecular level.  For example, we have seen that the elliptic shape of the ring opening is very important, as it can recognize the two different configurations of the terminal groups of the axles. This insight might help in the construction of light-powered molecular devices, of which these rotaxanes are important building blocks.

The results of this work are discussed in our paper (1), which is part of the ChemPhysChem special issue on molecular machines.  You may get a nice picture of the field by taking a look at this issue. Its contributions well illustrate the concept that molecular machines -especially natural ones – are incredibly complex and fascinating systems, and we are just beginning to understand their inner workings.

(1)G. Tabacchi, S. Silvi, M. Venturi, A. Credi, E. Fois, ChemPhysChem 2016, 17, 1913 http://dx.doi.org/10.1002/cphc.201501160

A brief summary of the article (with links to additional resources) may be found here.