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“.

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:

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…

 

How carbon monoxide binds to TiO2

What do a spacecraft, a breathalyzer, and carbon monoxide have in common? Nothing at all – you’d think. And you’d be wrong!  All three give you information on things that you cannot directly see, touch or measure. A spacecraft can capture some signal and send you beautiful images of a planet. With the help of a breath tester, a policeman may deduce the alcohol content in your blood. And using carbon monoxide, researchers may find highly reactive centers on materials surfaces.  Let’s focus on the latter and see how it works!

image1
Left image: the Soyuz spacecraft (source: Wikimedia commons). Center image: a breathalyzer (source: photograpy by Elza Fiúza/ABr, distributed under a CC-BY 3.0 license). Right image: carbon monoxide (blue=carbon; red=oxygen).

When a molecule comes in contact with surface atoms, its properties change. By measuring these changes, you get information on the surface sites interacting with the molecule.  Molecular vibrations – that you can measure by infrared spectra – provide very useful information: the vibration of carbon monoxide is very sensitive to the type of surface sites.  That’s why this molecule is used to identify active centers on catalytic materials, such as titanium dioxide.

How does carbon monoxide (CO) bind to surface atoms?  If you’re a chemistry student, you (should) know very well how CO interacts with molecules and ions. You’ve learned that this molecule can work both as a donor and as an acceptor of electron density.  Well, what’s nice, is that this happens also on surfaces, and  you can see it experimentally.

Let’s see this step-by-step. Carbon monoxide is a peculiar molecule. When it acts as a donor, charge flows to its bonding partner, which could be, for example, a metal cation.  This process strengthens the C−O bond and increases its vibration frequency.  This means that, in the infrared spectrum of the sample, you’ll find the CO band at higher frequencies – “blue-shifted” – with respect to the free, unperturbed molecule.  But carbon monoxide can also accept electron density from its bonding partner. If this occurs, the C-O bond becomes weaker: its stretching frequency decreases, and you’ll see a “red-shifted” CO band in your spectrum.

Carbon monoxide is colorless, odorless, and highly toxic – a true and unmerciful silent killer. It binds to iron(II) in hemoglobin, and this prevents the delivery of oxygen to the human tissues. This is a – very unfortunate – case where carbon monoxide acts at the same time as a donor and as acceptor. The bond is synergic: CO donates to the metal,  the metal back-donates to CO, and these two mechanisms reinforce each other:– that’s why it kills.  This synergy  occurs in many molecular complexes of transition metals and ions – often with less dangerous consequences. It’s less known on metal oxide surfaces, but it may happen as well. Is this the case of TiO2?

Not apparently, because carbon monoxide can only be a donor towards Ti cations –  they are Lewis acids, and cannot give back electron density.  The lower is their coordination number, the stronger is their acid power.  For example, a Ti cation coordinated by 4 oxygens  – Ti(4) – should be a stronger acid than one bound to 5 oxygens  -Ti(5).

Researchers use carbon monoxide to explore the activity of surface cations and deduce their environment, in particular the number of oxygen neighbors. This information connects the reactivity of a catalytic center to its molecular structure,  and may help them to improve the catalyst.  Practically speaking, they send carbon monoxide on a TiO2 sample and measure the infrared spectrum.  The rule is simple: the higher the frequency of the CO band, the more reactive are the Ti sites on the sample, and the lower their coordination number.

sitetio2
The image shows a 5-coordinated  Ti center (left) and a 4-coordinated  Ti site (right) on  anatase-TiO2 surfaces

So if you had a TiO2 sample with Ti(5) sites, and a second one with Ti(4), what would you get from the experiment?  “The second sample should show a more blue-shifted CO band, because Ti(4) is a stronger Lewis acid”.  If you answered this, you’d be wrong… because we actually did the experiment, checked with calculations, and found the contrary.  We found that CO on Ti(4) gives a less blue-shifted band – even if Ti(4) is a stronger Lewis acid.  Just as if a breathalizer estimated a lower alcohol content in a drunker driver. This could happen only if a sort of magic potion neutralized the effects of alcohol (something similar exist in real life, but it’s a mineral and belongs to the large family of zeolites). Similarly, our carbon monoxide on Ti(4) should have received an antidote against the loss of electron density. The antidote could only be electron density: but where did it come from?  Simply from the oxygen atoms bound to Ti(4): they are close enough to CO and ready to help.

In short, what happens is that CO donates electron density to Ti, but the surface oxygens donate electron density to CO. The first process strenghtens the C-O bond, but the latter has opposite effects. As a result, you find the CO signal at frequencies lower than expected.  The two mechanisms are sketched in the figure below – my attempt to explain in a simple way the two-fold nature of the Ti-CO bond on titanium dioxide surfaces.

theTiCobond2

So, if you see high frequency bands in an infrared spectra of CO, please be warned: not necessarily they are due to very reactive sites on TiO2 surfaces.  And also keep in mind that carbon monoxide gives you indirect information on your sample.  Its signal can be influenced in complex ways by several factors – you might misinterpret your data, based on simple rules. From a practical viewpoint, i think that you should be aware of this, especially if you’re working on CO, or titanium dioxide materials. More speculatively, this story might help us to better understand how molecules interact with surface atoms. The complex, delicate balance of molecular-scale interactions is at the origin of technologically important phenomena – reactivity, catalysis, photocatalysis, just to mention some of them.  Understanding these interactions more deeply could help us to improve their practical applications. Much effort is still needed, but it’s worth doing!

This research by our group has been published recently (Deiana et.al., ChemPhysChem 2016, 17, 1956; 10.1002/cphc.201600284). It was also sketched in a short summary, and by an infographics in a previous post.  Here i used other words to tell the same story, because i feel it’s important to make research results accessible to a larger community.