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.


Titania nanoparticles, carbon monoxide and infographics.

During this weekend i tackled a challenging task: to try to explain one of my recently published papers with an infographic. My first thought was to write a blog post (maybe i’ll do it as well), but i was intrigued by the idea of lumping a couple of years of work into a few tiny lines. Although attracted by the immediacy of infographics, i never used this tool, and it sounded just the right moment to give it a go. So, i went to the Canvas site and chose a fitness club advertisement as a template. After a bit of playin’ around, that’s what i’ve got:


I admit i’m quite happy with it, even if the making process was not plain sailing at all, at least for me. As a first-time user, i think that there’s room for improvement, and i’ll probably do some other attempts. Actually, i enjoyed creating this infographic!

I have published it (the infografic, i mean) in figshare (acceptance rate: 100%, publication fares: 0 €). That’s openaccess – free to download and use. Unfortunately, that’s not true for the paper – not enough funds to make it openaccess as well. Anyway, if you might want to give it a look, here’s the link:

Deiana, C., Fois, E., Martra, G., Narbey, S., Pellegrino, F. and Tabacchi, G. (2016), On the Simple Complexity of Carbon Monoxide on Oxide Surfaces: Facet-Specific Donation and Backdonation Effects Revealed on TiO2 Anatase Nanoparticles. ChemPhysChem. doi:10.1002/cphc.201600284

Another short explanation can be found here, with links to additional material.

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.

A ring (R)
An axle (EE)
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

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