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.

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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!
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My first computational chemistry lab

Teaching is an important part of my daily activity. It is time-consuming, requires a lot of energy and involves an emotionally intensive effort so, why not blogging about it?

Explaining  physical chemistry  to undergraduate students is by no means an easy task. Many students consider it too difficult -which is bad – and boring – which is even worse.  When last September i was asked to set up a new physical chemistry course from scratch, i went into panic mode. Mission impossible. How could i make this course interesting to students aspiring to become organic or analytical chemists?

Problem n. 1: The content. There were already several courses on theoretical chemistry. I wanted something different: with solid content, but new and appealing.  Two important topics were not sufficiently covered by other courses: electrostatics/electric currents, and intermolecular forces – quite useless and unexciting things, to students’ eyes. My idea was to show them that knowledge of those boring topics could unlock the door to molecular electronics and supramolecular chemistry. To make students willing to learn that stuff – quite an ambitious goal – I used examples, borrowed from the recent literature and even from my own research work.

Problem n. 2: The name.  Names of physical chemistry courses  often appear obscure and discouraging, to students. Fortunately I shared my worries with some colleagues, and, after some brainstorming, we converged on “applied physical chemistry: from molecules to devices”. Don’t know if this was a good choice – only time will tell. But all students of the master degree chose to follow it … because of the “applied”, i suspect. Anyway, that was a good start, at least.

Problem n. 3: The lab. That is, the practical part of the course. Why not a compchem lab? Despite being a computational chemist i never had the occasion of doing that before – i had to teach other courses  – and again i felt overwhelmed.  Many of the students had never seen any of the most basic Linux commands,  not even used a quantum chemistry code. Once again i shared my thoughts with colleagues, and looked through the web in search of suggestions. There’s a lot of excellent material, but, unfortunately, often too advanced for the needs of my students – most of them at their very first exposure to computational chemistry.

My solution was to schedule three 4-hour sessions. Very schematically, the objectives were the following:

1)  Learn the basic Linux commands, prepare  Gaussian-09 input files and run energy calculations for simple systems -a water molecule, a water molecule dimer, ethylene and benzene. Plot the electron density and the electrostatic potential surfaces and deduce from them the possible types of intermolecular interactions.

2) calculate by points the potential energy curve as a function of distance for a sodium cation interacting with a benzene molecule. Plot the curve and compare the resulting energy minimum distance with that obtained from a geometry optimization of the full system benzene-Na+.

3) (this was the most exciting part) – run energy calculations on components of molecular machines, e.g. small diazobenzene axles and crown ether rings, and try to discuss the possible intermolecular interactions between these components on the basis of the electrostatic potential maps. In the picture below, you can see the students actually doing such little exercise!

2016-06-09 10.56.40

I’m not sure that this was the right way to go. Of course, everything can be done better -some important issues, on e.g., accuracy and basis set choice, were necessarily swept under the carpet, but I had the feeling that the students sort of enjoyed their first approach to modeling.

 

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.

anello
A ring (R)
axe_trans
An axle (EE)
axe_cis
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 http://dx.doi.org/10.1002/cphc.201501160

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