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.

Movie_100_7

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“.

Water in hydrophobic and hydrophilic channels

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.

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X-ray structure of  ZL-MOF and zeolite L, viewed perpendicular to the channel axis. In both materials, the water positions (cyan spheres) are partially occupied

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.

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Optimized structures of ZL-MOF (left) and zeolite L (right), viewed along the channel axis. The hydrophobic methyl groups of the MOF (in gray) protrude inside the channel and force the water molecules to arrange in well-separated rings. In the hydrophilic channels of zeolite L, a continous water structure is formed.

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.

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Optimized structures of ZL-MOF (left) and zeolite L (right) (front view). While the water rings in the MOF are dominated by water-water hydrogen bonds, the water molecules in zeolite L can interact very strongly also with the potassium cations (purple spheres) and the framework.

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.

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Water rings in ZL-MOF (left), and water pre-dissociation complex (in red) in zeolite L (right)

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.

On #RealTimeChem and #CompChem

Because chemistry is beauty, and you want to show it,

Because chemistry is exciting, and you like to share it,

Because chemistry is diverse, and you want to contribuite,

Because chemistry is community, and you feel to be part of it:

there’s #RealTimeChem: the greatest community of chemists on line . As @Doctor_Galactic says, it “exists to celebrate chemistry day or night” because chemistry happens any time: it’s done by real people, and it’s part of our life.

As much as you enjoy celebrating chemistry, doing research and running experiments, it  comes a moment when you feel tired, disappointed, or sad. Sure, we all have those moments – and when they come, the warmth of the community might do a great deal (trust me – it works)!

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The banner of the event, designed by @compoundinterest

Although the #RealTimeChem hashtag “operates 24/7“, there’s a special time of the year: the #RealTimeChem Week, aimed at raising awareness of the community and encouraging chemists of any level and discipline to join in. By following #RealTimeChem, you see lots of cool chemistry,  and the fun is doubled if you also take part. It involves a “competition” with different award categories (sponsored by C&EN ), and other fun activities, like a creative chemistry cooking contest (sponsored by @ChemPubSoc_Euro), or a blog carnival. This year I am particularly excited, because i happened to be among the winners (thanks C&EN!) and this made my day.

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Nonetheless, taking part and being inspired by all the great chemistry outside there, was equally exciting – both fun and instructive. For a taste of the awesomeness of the event, please take a look to this beautiful article from C&EN (which also contains fab pics from the winners/runners-up of all categories), or to Doctor Galactic’s blog , where you may find “delicious” images from the winners of the #Whatscooking? contest!

This is the right occasion to celebrate #RealTimeChem  for bringing together people actively doing (or curious about) chemistry, its inventor Dr. Galactic, all the organizations supporting the amazing activities, and everyone that post their fun/inspiring/unexpected/awesome contributions to #RealTimeChem.

This year the theme of the week (as suggested by @g_laudadio  and chosen by the community) was #Chem4Life – the chemistry of every day life. Being a computational chemist, I find it often hard to share my “everyday chemistry” with lab colleagues, especially those working with colourful transition metal complexes, or beautifully fluorescent stuff.  Of course, nice molecular graphics or three-dimensional orbital plots nowadays help a lot to raise interest in theoretical/computational chemistry (#compchem), but what happens behind the scenes? What actually is “everyday #compchem”? The pictures I shared on Twitter were an attempt to capture such an aspect in a visual, immediate way! Here is it:

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Wavefunctions in minimalist look!

As regards the #compchem hasthag, it has been around for long time. It is used among #compchem -ists to exchange research news about #compchem papers or codes, but also as a discussion forum, to ask for advice, to advertise a PhD or postdoc position… and so on.  There is also a “community journal” named Computational Chemistry Daily, maintained by @janhjensen , to which everyone can contribute by tweeting a link to a paper (or to a code, blog post, graphics..) using the hashtag  #compchem. It is extremely useful for keeping up with the field: I see it as a sort of community service, and love it. I’ve learnt a lot by following it, and met awesome people! It’s important for the computational/theoretical chemists of all ages, levels, and flavours of #compchem to have an informal place where they could meet and discuss. And I am grateful that this place exists…  thank you so much all of you awesome #compchem-ists!

“Everyday #compchem”

pseudopotential

 “beautified #compchem” 

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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….

 

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.

step01

Fortunately, modeling comes to the rescue…. and that’s one of the reasons why I love so much doing #compchem (computational chemistry)!!

step02

Step 2 revealed that the channel openings expose hydroxyl groups, and look somewhat like this:

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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.

stopcoc

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.

step03

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…

step05

… 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.

zeolite_channel_openings

 

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.

Senzanome
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

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.

 

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