An enigmatic proton

The best superpower ever? Being invisible, of course. How nice it would be to wear a magic cloak and escape boring meetings. Too bad that these tricks work only for ghosts, magicians, and superheroes. But in the atomic world, things are different. In this realm, our superhero is the smallest atom of the simplest organic acid: the proton of the formic acid molecule.

Many green chemistry applications involve organic acids and titania. So, the reactivity of formic acid on this material has been much explored, but its acid proton has escaped the most accurate experiments so far. Where is the missing proton?

By using computational methods #compchem, we’ve seen that the proton is shared between one oxygen of the formic acid molecule and one oxygen of the titania surface. At very low temperature, sharing is governed by real superpowers quantum effects, while, at room temperature, the proton moves very fast between the molecule and the surface – to see it in action, look at the movie!  Anyway, in both cases, “sharing is caring”: it makes the acid proton “invisible” to experiments and protected from the attacks by bases.

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The surface of titania acts like a protecting group for the formic acid proton. How does this work? Formic acid shares its proton with the surface, so it’s very difficult for other molecules to take it away! This protecting action of the surface could explain, for example, why carboxylic acids on titania, upon addition of amines, give high-value products (amides) at low costs for the environment.

Last_vdw_TocDiscovering the fate of the missing proton was a joy for my #compchem-ist’s eyes.  Perhaps, it might become also useful for applications: indeed, it is just the acid proton that makes carboxylic acids on titania so interesting.  Next step would be to study this process on different surfaces of titanium dioxide. This could help to understand how defects affect the reactivity of the acid proton.

On a personal note, my feeling is that our work has unveiled just a small part of the wonderful things that molecules can do on surfaces. But it’s so nice to find, from time to time, a little pearl in a shell.

coversimple2Thanks @andrea_stangoni for designing such a marvelous artwork, thanks @angew_chem for this great honor, and for your lovely “sharing is caring” pun. We’re grateful to @ChemRXiv for hosting our preprint, all the people giving feedback on it, and the reviewers of the paper. No external funders to thank, this time. Instead, we send love to our old #compchem machines – the resources of a tiny group from a little institution planet in the Galactic Empire’s periphery.

The pearl in a shell also reminds me of a mollusc without shell. Along its 4y+ life, our project has faced abundant failures and rejections – yes, the familiar “been done already, nothing new, not worth financing” story,  plus “simulations are, at best, an useful add“. No protective shell, and no Harry Potter’s cloak in those days. Yet, all those failures, critical comments, and rejections – even the most painful ones – prompted us to sit back and ponder previoulsy unseen aspects of the problem – and then, to work harder and deepen the analysis. This improved our work considerably.  Also, posting a preprint on ChemRxiv gave us strong moral support during the final stages of the work. 

We’ve all been there – things don’t always go as planned, and often let us down. But muggle tricks like persistence, faith, and time to cleanse mind and body spent on Twitter help a lot. My message? Keep calm and don’t give up: as someone else has said,  Hard times come, hard times go, yeah just to come again“.

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

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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.

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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:

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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….

 

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.

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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.

perylene

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

High pressure and small spaces create order from disorder

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:
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Many thanks also to my institution, @Uni_ Insubria, for issuing a piece on our research and sharing it on the social media. The Uni_Insubria release – including also an English translation, can be found at this Facebook link  (Italian version also at: Chemistry & Earth Science Department of Uni Modena-Reggio Emilia – that we thank as well).