physical chemistry

Molecular view of a common sunscreen

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Wearing sunscreen everyday decreases your risk of skin cancers and helps your skin maintain a healthier look. But how does a sunscreen work? The chemistry of a sunscreen lotion, nicely pictured in this infographics, is actually quite a complex matter. The key ingredients are molecules known as UV-filters, which can absorb UV light and then dissipate the energy harmlessly in the form of heat.

Octinoxate is one such molecules. The active part contains a ring system and conjugated double bonds. It has a flat structure – denoted as “trans“- and excellent UV-B filter properties. Unfortunately, its filtering action is degraded by light over time. Under sunlight, the molecule is converted to a less effective form, named “cis“. Understanding why this process occurs might help to improve the efficacy of sunscreen lotion and creams.

Chemical structure of trans-octinoxate (octyl methoxycinnamate). The left part of the molecule acts as UV-filter, while the right part – the alkyl chain – ensures optimal mixture in sunscreen lotions. https://commons.wikimedia.org/wiki/File:Octyl_methoxycinnamate.svg

We studied with accurate calculations the two forms of the octinoxate molecule. In contrast to what was previously thought, the less active cis form is slightly more stable than the commercially valuable trans form. This finding explains why the UV filter loses efficacy, and may suggest possible ways to limit the degradation processes.

The two forms – or isomers – of the molecules have very different shapes. The trans is approximately flat, as shown in the left picture, while the cis is bent, as illustrated in the right image.

In cis octinoxate, the alkyl chain folds over the other part of the molecule, leading to a more compact shape, stabilized by dispersion interactions. Practically, the chain plays a key role, because it allows the filter to be easily dispersed in the lotions and creams we commonly use to protect our skin.

More technically, these subtle effects, highlighted by post-Hartree Fock calculations, are not fully captured by density functional approaches. All the tested functionals, including the B2PLYP double hybrid, predict the trans structure to be more stable than the cis one. This molecule is indeed a challenging system for any computational approach.

The striking difference of shape between nearly flat trans-octinoxate and folded cis-octinoxate suggests that this change of shape might help to dissipate the energy accumulated upon light absorption. Perhaps, this effect might also be beneficial to the sunscreen action.
As a further step to understand the peculiarity of this molecule, the cis– and trans- forms of octinoxate could be also investigated via molecular dynamics simulations to better capture the differences in their complex behaviour.

Links to the article , the free accepted manuscript and preprint version.

An enigmatic proton

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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“.

On #RealTimeChem and #CompChem

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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)!

Cattura
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.

REALTIMECHEM

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:

realtimechem
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” 

zeolitel

Porous materials, minerals and bees

~ moleculardreams ~ 2 Comments

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. 

P1270522
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.

front_low_res
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:

Wchain
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.

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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:

zeoliteLChannel
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

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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

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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.

 

twitter2018_3_b

High pressure and small spaces create order from disorder

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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:
mrs_42_3_175-179-March17.indd

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).

Under pressure, from chaos to order.

~ moleculardreams ~ 4 Comments

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.

Perspectives

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.

Reference: Irreversible Conversion of a Water–Ethanol Solution into an Organized Two-Dimensional Network of Alternating Supramolecular Units in a Hydrophobic Zeolite under Pressure, by Rossella Arletti, Ettore Fois, Lara Gigli,  Giovanna Vezzalini, Simona Quartieri, and myself. Angewandte Chemie 2017 – DOI:  http://dx.doi.org/10.1002/anie.201610949
http://dx.doi.org/10.1002/ange.201610949

Special thanks to Andrea Stangoni (@andrea_stangoni), author of the cover artwork.  His image summarizes the ideas of our work much more beautifully than my blog post!

ange201700219-toc-0001anie201700219-toc-0001-m

And, of course, big thanks to Angewandte too! 🙂

Here are the official versions of the cover:

http://dx.doi.org/10.1002/anie.201700219
http://dx.doi.org/10.1002/ange.201700219

Hope you enjoyed the movies, both (equilibration and final) available at figshare.

Update:  the green open access (accepted article) version of this paper is now freely downloadable from the figshare repository.

How large molecules cross narrow pore entrances

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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.

newchannel
Chem. Commun., 2016, DOI: 10.1039/C6CC05303C
Acknowledgments
 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.
Update: 
Many thanks, of course, also to ChemComm for the cover!
cc_cover