Porous materials, minerals and bees

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

The regular cavities of zeolites do a great job in organizing guest 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.

Molecules in nanocavities are sort of like bees in a honeycomb: they form an organized colony (Artwork: Andrea Stangoni)

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:

Water wire found in the channels of a natural zeolite

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.

For more information….


The devil makes the pots but not the lids.

il diavolo fa le pentole ma non i coperchi

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.

Our containers are named zeolites – porous materials which are commonly used as adsorbents and catalysts in various commercial, industrial, and even medical applications as well as in our everyday life.  Also, if you fill zeolites with dye molecules, you’ll get materials able to capture and transfer solar energy very efficiently. You would do it much easier if you first know how their pores look like.

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:

Entrance of zeolite L channel, showing the terminal -OH groups and the channel accessibility.

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.
    In particular:

     – 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.



For more information…


Understanding an efficient light harvesting material

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.

Perylene-bisimide dye (cyan) in zeolite L (gray). The purple spheres represent the zeolite potassium cations

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.


Gigli et al. (2018)  “Structure and Host–Guest Interactions of Perylene–Diimide Dyes in Zeolite L Nanochannels”  J. Phys. Chem. C 122, 6, 3401-3418

RSC Twitter conference 2018

The Twitter Poster Conference is an annual event organized by the Royal Society of Chemistry, which consists of sharing chemical research using tweets. You may take part either by tweeting an image of your poster or by commenting on other poster (doing both is better, in my view). As in a traditional conference, you see great research, are asked interesting questions, meet old friends, and come in contact with new colleagues or potential collaborators. Only, at the twitter conference this happens 24 hours non-stop  on global scale; so, it’s a good idea to get there prepared!

I enjoyed so much my 2017 participation that I couldn’t miss the 2018 edition.  Of course, it was awesome, and I am grateful to the organizers, the sessions’ chairs, and all participants, particularly those with whom I interacted.  Indeed, I have learnt new stuff, seen exciting science, been inspired, without moving from my office and paying any conference fees. Really cannot ask for more. Many thanks to all of you!

Tweeting posters is not trivial. For optimal readability,  you should keep into account, for example,  that mobile phones have small screens, and that Twitter images are resized and cropped down – so, it would be better to prepare the poster in landscape format. These and other useful tips can be found in this excellent post. I came across it when the event was over, but it would surely be useful in the future.

Below you can find my poster, illustrating the fruitful collaboration between calculations and diffraction experiments at high-pressure conditions.

Besides water and ethanol in ferrierite (discussed in this post), the poster shows our new work on a host-guest compound of zeolite L and fluorenone dye under high pressure. These host-guest materials have excellent optical properties, useful for many applications, from solar cells to sensing in medical technology. Knowing their structure and working principles could help improve their performances – that’s why we try so hard to understand dye-zeolite composites at molecular level.

Basically fluorenone inside the channels of zeolite L forms a molecular ladder, which is very stable at room conditions because the carbonyl groups of the dye interact very strongly with the potassium cations of the zeolite.

Is this peculiar structure also stable under GPa pressures?

According to experiments and simulations, the answer is apparently yes!  Our composite  maintains its structure, and the interactions between the dye and the zeolite cations become stronger. The exceptional resilience of this material to compression highlights its outstanding mechanical properties. These are important to extend the application of dye-zeolite composites beyond room-pressure conditions.

More about this research can be found in this recently published paper (“Unravelling the High-Pressure Behaviour of Dye-Zeolite L Hybrid Materials”) – which is open access. The high-resolution poster and the green open access version of the ferrierite paper can be downloaded at figshare.



RSC Twitter poster session 2017

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.

To those of you that might wonder what a twitter poster session is, here’s an excerpt from The Analytical Scientist:

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.

Just for the records, here’s my humble contribution to #RSCposter.  For those interested, what featured in the poster is briefly explained here (left side) and blogged here (right side).