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…


How large molecules cross narrow pore entrances

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.

 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.
Many thanks, of course, also to ChemComm for the cover!

Titania nanoparticles, carbon monoxide and infographics.

During this weekend i tackled a challenging task: to try to explain one of my recently published papers with an infographic. My first thought was to write a blog post (maybe i’ll do it as well), but i was intrigued by the idea of lumping a couple of years of work into a few tiny lines. Although attracted by the immediacy of infographics, i never used this tool, and it sounded just the right moment to give it a go. So, i went to the Canvas site and chose a fitness club advertisement as a template. After a bit of playin’ around, that’s what i’ve got:


I admit i’m quite happy with it, even if the making process was not plain sailing at all, at least for me. As a first-time user, i think that there’s room for improvement, and i’ll probably do some other attempts. Actually, i enjoyed creating this infographic!

I have published it (the infografic, i mean) in figshare (acceptance rate: 100%, publication fares: 0 €). That’s openaccess – free to download and use. Unfortunately, that’s not true for the paper – not enough funds to make it openaccess as well. Anyway, if you might want to give it a look, here’s the link:

Deiana, C., Fois, E., Martra, G., Narbey, S., Pellegrino, F. and Tabacchi, G. (2016), On the Simple Complexity of Carbon Monoxide on Oxide Surfaces: Facet-Specific Donation and Backdonation Effects Revealed on TiO2 Anatase Nanoparticles. ChemPhysChem. doi:10.1002/cphc.201600284

Another short explanation can be found here, with links to additional material.

disassembling molecular machines

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.

A ring (R)
An axle (EE)
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

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