CSD Educators: Alessia Bacchi from Università di Parma

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Written by

Ilaria Gimondi

Posted on

April 22, 2021

For this CSD Educators blog, I have the pleasure to introduce to you Prof. Alessia Bacchi, from the University of Parma in Italy. In this blog, Alessia will talk to us about her recent experience teaching "virtually" the use of Mercury and the CSD in high schools, with the goal to help students and teachers with the learning and teaching of three-dimensional concepts, such as the geometry of molecules.

Alessia is not only passionate about crystallography (so much that she is currently the Vice-Chair of the CCDC Board of Trustees!), but also about outreach and divulgation. Over the years, she was national coordinator for the activities of the International Year of Crystallography (2014), she curated the exhibition CRISTALLI! in Parma (do you remember the picture about it from this blog?), and she established the Museum of Crystallography at the University of Parma (2015). It is great to see in her blog the CSD being used in high schools, really inspiring and supporting the next generation of scientists and crystallographers!

 From Alessia Bacchi from the University of Parma, Italy

We all remember the sheer excitement of our first experience in seeing and being able to rotate molecules on a screen, the curiosity to explore molecular architectures, the beauty of the perfect planarity of aromatic rings, and the sense of wonder and awe watching the fantastic variety of structures in scrolling through the CSD.

Two of my favourite quotes which reflect the rich experience of admiring chemistry’s most beautiful buildings are form two of the greatest scientists in the field of structural chemistry:


“I became captivated by the edifices chemists had raised through experiment and imagination-but still I had a lurking question. Would it not be better if one could really 'see' whether molecules as complicated as the sterols, or strychnine were just as experiment suggested?” (Dorothy Hodgkin, Nobel Prize Lecture, December 11, 1964, https://www.nobelprize.org/uploads/2018/06/hodgkin-lecture-1.pdf)


 “I think that the great ocean of truth is still in front of us and that we will continue to discover new aspects of this truth” (Olga Kennard, J. D. Bernal Lecture, 1995, Birkbeck College)


I think that this an extremely powerful engagement point for young students, and their teachers as well.

We tried to leverage onto these concepts in tackling the problem of the scarce sense of three dimensional spatiality that students reveal when they learn the concepts of chemical bonding. In fact in the last years we have noticed that first year university students are somehow loosing skills related to the description of three-dimensional molecular structures: confounding the concepts of linear and planar, or not being able to assess angular values are examples.

When asked to build a 3D model of hybrid atomic orbitals with plasticine, in a sort of bricolage challenge during the lectures on chemical bonding, many students were unable to properly execute the task.

We can track back to, and share with, high school the problem of learning tools and methods, where the concept of structure in chemistry is often compressed in few hours, with no practicals attached to the enumeration of geometrical rules. The massive appeal to remote teaching experienced in the last two years has surely worsened the problem, loosing the possibility to at least actually show 3D models in the class (at the University of Parma we have a Museum of Structural Chemistry, Museo di Cristallochimica, to help students to metabolize 3D concepts, but the extended lockdown has prevented also the use of this permanent support).

Detail of a gallery of the Museo di Cristallochimica (University of Parma)

Detail from a gallery of the Museo di Cristallochimica (University of Parma). 


The educational resources offered by the CSD can help to mitigate this problem. In March 2021 we organized an online 'learn-structural-chemistry-by-using-mercury' tutorial for high school students and teachers, within a specific program of knowledge exchange between the University of Parma and high schools. The title of the tutorial was “Architetture alla nanoscala: come visualizzare le molecole e i cristalli a casa propria” (“Nanoscale architectures: how to visualize molecules and crystals at home”).

We had 113 registrations, of which about 80 actually attending, from high school 4th-5th year students, with some background in chemistry. Four teachers attended as well with their classes. The aim of the tutorial was to teach students, together with their teachers, to actively use Mercury for understanding structural concepts linked to chemical bonding and to weak interactions between molecules.
We pre-divided the registered students in 4 teams (usually one class = one team). Each team had to define one-two leaders and a teacher, who were provided with the installation of Mercury a week in advance (about 20 people, including some who registered and played individually). No one had problems in this phase.
On the day of the tutorial, I presented Mercury and guided a demonstration about the structural information that can be gained by analysing bond geometry, planes, and crystal packing of aspirin (ACSALA). I showed also how to retrieve information on the molecule by searching the refcode on WebCSD. Those provided with Mercury followed on their computers step-by-step, the others watched on my shared screen.
After this, we divided the teams into separate virtual rooms, and they chose one other example from a list of cifs that I gave them (drugs, explosives, food... etc). Then, they had to identify the molecule using the refcode and WebCSD, and discuss together within the team with the help of those who were using Mercury, and compile a report writing down the structural description of the molecule and of the crystal packing, with figures (very basic concepts, of course). We provided a guided template to facilitate the report, with questions and items to analyse. Finally we taught them how to 3D print their molecule.
The total time of the meeting was 2h30, taking approximately 1h30 to introduce the workplan and illustrate how to use Mercury, and 1 hour for the teams to execute their tasks. A total of 4 tutors, one per virtual room, were involved assisting for technical problems or suggesting how to move on.
The teams prepared a final report on their structures, and we reconvened after some days to discuss their results. Students learnt how to measure distances and angles, and how to assess planarity. They were able to grow the crystal packing by identifying and expanding intermolecular interactions. They learnt how to produce pictures illustrating structural features.


The task of reporting based on structural evidence resulted not a easy one for the students, who sometimes tended to rely on their previous knowledge to answer, and then used a picture to support the answer. One example was the concept of chirality: while the report declared that the studied molecule was chiral based on the chemical diagram, the chiral carbon was not easily identified in the 3D molecular structure on the screen. This has shown how much a visual approach supporting concepts can be needed in high schools and university first year classes.


Teachers were extremely aware of this gap, and they have been highly engaged in the activity. The hope is to share with high school teachers a culture on how to use Mercury to illustrate simple chemical concepts.

More information

The list of the CIFs used, the template of the report and initial instructions on how to install and test Mercury are available from Alessia (in Italian) for colleagues who wish to repeat the experience.

Ed: If this blog inspired you, explore the free version of Mercury (here) and the free Teaching Subset (here) to use for your teaching and outreach activities!


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