Water. Always difficult to write something original about it, but let’s spend again a few words in celebration of this molecule. Water is present, or can be inserted in many porous hosts, like zeolites or MOFs. Not all of them love water. This time the question was: what does water do inside channels of similar size but different hydrophilicity?
We modelled the behaviour of water in two porous materials. The first one is zeolite L, which is hydrophilic. The second one is a metal organic framework, or MOF, which has pores of similar size, but less affinity to water. Our starting point was the X-ray structure of the two materials, shown below.
The water distribution inside the pores looks very nice and symmetric. Unfortunately, the water positions are only partially occupied. So, by using the experimental water content as input, we optimized the structure of these materials, and here’s what we got.
We found that water stabilizes both materials, and that the shape of the water clusters inside the channels depends on the affinity of the hosts to water.
While the hydrophobic host contains water rings, kept together by water-water hydrogen bonds, the hydrophilic host contains a continuous water tube, stabilized by interactions with the zeolite and also by hydrogen bonds.
In the zeolite channels, some water molecules are surrounded by five strong hydrogen bonds. This structure is similar to water pre-dissociation complexes found in liquid water, and it might probably explain the high proton activity found in zeolite L.
Zeolite L is a promising material for solar cell applications, but the high proton activity inside the channels might damage some of the organic dyes that are incorporated as guests. Now we have identified a possible cause of the problem, and this might be a first step to improve the performances of these materials. Also, we hope that the atomistic insight on the water rings inside the MOF could help to exploit this material as host matrix for new compounds.
Personally, I much enjoyed doing this work: there’s always something to learn about confined water! The “driving force” for starting this work was an invitation, so many thanks to Michael Fischer and Robert Bell for organizing the Special Issue“Modelling Crystalline Microporous Materials” in the Zeitschrift für Kristallographie. If you like porous materials and #compchem, please have a look at this issue, it has many beautiful contributions. Also, thanks to ChemRxiv for hosting our preprint, and to the 2019 Twitter #RSCPoster conference, where this work was first presented as poster.
Overwhelmed with the increasing flow of new scientific discoveries and related literature? You’re not alone. We live in the information overload era: too much to read, too little time, and life is short. Probably we’d need more readable, shorter papers too. Why writing a long one? Perhaps, it might connect disciplines which speak different languages but have much in common. Like material science and mineral science.
Let’s start from the first one.
You can make materials for solar cells, optical devices or medical sensors by trapping molecules or nanoparticles inside a “host”. Once there, molecules are no longer free to move, like in a gas or a liquid. This process, called “confinement”, brings to life new properties, which were not present in the individual molecules and are very useful in technology. Energy transfer or information storage, for instance, are made possible by the organization of the confined molecules.
Tiny smart objects such as molecular machines, motors and diodes, make good use of self-organization processes, which create order from apparent disorder by exploiting interactions between molecules. This task gets easier when molecules are confined in regular pores. Think of a buzzing swarm of bees, first frantically hovering in the air, and then accommodated in a honeycomb.
Similar to honeycombs, regular patterns of pores like those in zeolites can orderly accomodate small molecules or clusters. But if you want to entrap, say, enzymes, peptides, or large nanoparticles, you must use materials with larger pores. Some porous silicas have large honeycomb channels, while the cavities of metal organic frameworks display an amazing variety of size and shape. With those nice architectures awaiting to be filled, ordering molecules might appear like an easy task.
As you imagine, things are more complex. Perfect order cannot be achieved. All cavities would need to be uniformly occupied by the guests. This is going to be very unlikely, because molecules move a lot even when they’re confined… like bees in a hive.
About bees, I had direct experience… as a child, I used to observe my dad opening up his hives to inspect them. This gave me the chance to “study” the behaviour of these awesome creatures inside their honeycomb.
Bees do not occupy all hexagonal holes in the frame, and move continuously around, without any apparent pattern. Hence they’re not perfectly ordered. In spite of this, the colony is amazingly organized, and performs an impressive number of complex tasks…. not just honey production!
Similarly, guest molecules confined in porous cages are not rigorously ordered. Yet they are organized, and the resulting host-guest materials can perform useful functions, which were absent in the free molecules. They can, for example, absorb and transfer photons like the antenna systems of plants and bacteria.
Now, the question is: can we improve the organization of the molecules and the performances of the materials? Well, first we should know how the molecules occupy the cavities, their orientation, spacing and so on. Are the guests aligned? Are they attached to the pore walls? What happens if water enters the pores? To find those answers, you should use several different techniques: each experiment will give you some pieces to compose the puzzle. And yes, computational chemistry helps a lot to figure our what happens inside the pores. Yet this remains a very difficult problem.
This is where mineral science might help.
Regular patterns of cages are very common in the mineral world. Not long ago, for example, geologists found in Antartica a mineral with the same structure of zeolite Z-SM5, a well-known and widely used artificial industrial catalyst. That was indeed a big surprise! Natural zeolites are indeed amazing: their pores contain impressively stable structures formed by small molecules and cations. Just look at this water wire:
Contrary to what you’d expect, this chain is incredibly resistant to heat and pressure. First found in a rare mineral, it was named “one-dimensional ice”. But actually, our water wire “melts” at about 340 C inside the mineral framework! This is a great example of organized structure made by Nature. You can find many others: the most famous ones are perhaps gas hydrates. Several silica minerals have hydrate structures, which are also very common in man-made porous materials. Indeed, we should pay more attention to the close links between natural and artificial host-guest materials.
Natural porous minerals, the intriguing organization of their guests, and their response to mechanical stress can be an awesome source of inspiration in the quest of more robust and efficient materials. High pressure experiments with zeolites (and also some MOF’s) have already brought us new organized materials, along with many curious facts. But there’s so much yet to be discovered.
Perhaps, the problem with us (me included) and with our scientific era is that we don’t take enough time to relate with other disciplines. I’ve been so lucky to work with many awesome colleagues from the mineral, chemical and material science communities over the years, and it’s thanks to them that I wrote this review. One thing I learnt is that we should always try building bridges and strenghtening links between different fields because there’s nothing to lose, all to gain from a deeper exchange of ideas.
The title of this post is the literal translation of a proverb. The proverb means that Devil’s pot of wickedness sooner or later will boil – and, as there’s no lid, someone will see its content and reveal the truth. That’s the old innocent idea that, finally, justice will prevail over evil… well, I like it so much I use it as title. Rather than devils, this post is actually about pots and lids – of molecular size, of course.
As that’s not a Masterchef contest at the nanoscale, let’s get rid of the pot for the moment, and call it ‘container’. In the nanoworld there are many such containers, which can be filled with molecules. In this way, you can produce new materials with applications in various areas of technology: from solar energy to sustainability and human health.
In particular, how do their entrances appear to an incoming molecule? This question is our “step one”, because this information is really hard to get from experiments.
Fortunately, modeling comes to the rescue…. and that’s one of the reasons why I love so much doing #compchem (computational chemistry)!!
Step 2 revealed that the channel openings expose hydroxyl groups, and look somewhat like this:
Those terminal hydroxils can be condensed with other molecules, carrying specific groups, hence new properties and functionalities. Among them, the possibility of “closing” the pores. Why is it so important?
Zeolites are resistant to heat and pressure, and act as a protective shield around the dye. But every “pot” needs a “lid”: plugging the zeolite pore entrances, so that the dyes, once included, cannot escape into the environment, would further enhance their stability. This has already been done experimentally, by attaching at the channel entrances peculiar molecules nicknamed “stopcocks”. They consist of two “parts”:
the “tail”, which can penetrate zeolite pores;
the “head”, which is too big to enter the pore and remains outside, thus blocking (at least partially) the channel opening.
Two typical stopcocks, one with a small tail, and the other with a long, bulkier tail, are shown below.
Such “molecular stoppers” do indeed a great job in preventing molecules to escape from zeolites. However, there were no clear ideas about how these stoppers were attached to the pore entrance, and how much space they occupied. This knowledge would help finding better “lids” for our zeolite “pots”. How do we get it? Of course by modeling, as sketched in step 3 and 4.
Here’s what we learned:
stopper molecules prefer to bind aluminum sites at the channel entrance;
the tail group always penetrates inside the pore, while the head stays outside;
the extent of blocking depends on the stopcock.
– small-tailed stopcocks are like partially opened “lids” : no full closure – bulky-tailed stopcoks behave like “corks”: full closure
So the zeolite pore may be fully sealed by one bulky stopper, like a molecular cork on a Prosecco nano-bottle. On the contrary, one “lid” (small stopper) leaves our “pot” partially opened. Fortunately, there’s enough room to attach a second small stopper to the opening, that can now fully be closed.
And this brings us to step 5…
… which could well be the end of this story, first told some time ago. Thank you for reading it!
Anyway, there’s an epilogue, which is perhaps the nicest part (“dulcis in fundo“). Using such information, obtained from modeling, experimental colleagues recently trapped indigo (that’s, your denim’s blue) in zeolite L, and blocked the channel entrances with two small stopcocks. In this way, they made a new pigment, exceptionally resistant, with an amazingly beautiful blue color. For me #compchemist, that blue was simply….. the color of happiness.
When we fill porous materials with dye molecules of the right size, we obtain useful compounds for solar energy technology. These compounds can transfer solar energy efficiently because pores and channels fit to the dyes “like a glove”. In this way, molecules are forced to stay in line, and energy can easily pass from a molecule to the next one in the line. If we knew in detail the structure of the dye arrays, we’d have better chances to improve these compounds.
Unfortunately, the precise positioning of the molecules inside the pores is very hard to determine. Recently, we solved this problem for a class of particularly efficient dyes filling the channels of zeolite L. Key to success was diversity within the team, which favored the combination of multiple techniques involving both experiments and calculations.
The useful properties of these materials arise from the arrangement of dye molecules inside the porous host, which depends on the interactions among molecules and with the porous host. After this work, now it seems we understand a little better these complex materials. Indeed, our dyes are linear, symmetric and fit to the zeolite channels. Yet they adopt a slightly asymmetric positioning to maximize the interactions with the zeolite cations, which stabilize the compound.
This work also suggests some possible ideas to improve these compounds by modifying either the porous container (the “host”) or the dye molecule (the “guest”). In my view, this is also a good example of how computational modeling may help to rationalize experimental results in apparent contrast with each other, yielding a consistent picture of a useful and intriguing material.
On March 20th, i took part to the RSC Twitter Poster Conference 2017, an online event organized by The Royal Society of Chemistry to favour new contacts and exchanges among researchers in chemical sciences. The event was a big success.
How do Twitter poster sessions work?
Participants tweet an image of their poster with the title and hashtags #RSCPoster and the area (e.g. #RSCAnal) at any point throughout a 24-hour period. This means that people anywhere in the world can join in.
It’s a fully global event open to every chemist on twitter. No conference fees: by following the hashtag #RSCPoster, anyone could attend and submit their poster.
What a nice surprise when nice images of posters started appearing in the feed on that Monday morning. Awesome idea – i thought, tweeting my contribution a few seconds later.
To be honest, the poster was not prepared for the occasion – I simply recycled a poster presented at a traditional conference, and I shared it just to see what would happen. It was great. Not only people were tweeting their images, they were also commenting on the posters, just like in a standard conference but within 140 characters. The participants were discussing technical aspects of the results or methodology, asking more general questions on the featured research, and all of this worked wonderfully. It was exciting: every few seconds, a new contribution was added to the feed, containing interesting and well presented science.
As in normal conferences, this wasn’t just a chance to present your own project, but also a fantastic opportunity to look at what the researchers out there were doing, and to learn a lot from it. New ideas were inspired by work in apparently unrelated research areas. Beside science, it was also a very useful experience in communicating research to a heterogeneous audience using few, carefully selected words. Yet another demonstration of how twitter can be useful to scientists!
I regret that i wasn’t able to look at all the posters during the session – they were definitely too many. Fortunately, even if the conference is over, the posters are still hanging on the virtual wall at the RSC Tumblir site, so that in the case you missed the event, you might still catch up with the interesting science. I’d strongly recommend to give a look at them: they’re awesome!
Some lucky participants got the coolest thing you could ever imagine: a cartoon abstact of their poster – like this one:
So I’m very grateful to @MCeeP (ErrantScience.com) for making my day with this, and for the incredible tour-de-force of drawing the cartoons! I much enjoyed to see all of them: not only they were funny, but also further engaged the participants, stimulating curiosity and new conversations. These brilliant poster abstracts really made the conference unique.
This is crazy but …what if cartoon abstracts were introduced in traditional conferences as well? To get a feeling, just check out the complete gallery of these cool cartoons of posters at ErrantScience.
Finally, many thanks to the RSC, the organizers, and the participants for such a great experience. A superb way to promote chemical research. I’m glad to have been some little part of it, and looking forward for the next year event.
Our work on ethanol and water in ferrierite, published here and blogged in my previous post, has been recently covered by MRS Bulletin in an excellent news article – “High pressure and small spaces create order from disorder” by science writer Tim Palucka. Some time ago, I had a very pleasant communication with Tim about the main ideas and results of the paper. That interview also helped me a lot to understand how science communication is done professionally. The piece by Tim really does a great job in explaining the scientific background, the main findings and the perspectives of our research – and, of course, all of us are so happy about it!
MRS Bulletin contains other interesting news articles, which are very useful to get a first impression about what’s going on in the many diverse areas of materials science – we’re very proud to be featured there! Big thanks, therefore, to MRS Bulletin and Dr. Palucka for the awesome coverage, and to Prof. Gion Calzaferri for commenting on our work as an external expert. A pdf version of the news article is freely available at MRS Bulletin (Volume 42, Issue 3, pp. 176-177, DOI: https://doi.org/10.1557/mrs.2017.38 ), while the illustration showing the arrangement of water and ethanol in the zeolite is just here below:
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.
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.