CSD Educators: Natalia Alvarez from Universidad de la República, Uruguay

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Written by

Ilaria Gimondi

Posted on

March 25, 2021

It is my pleasure to welcome Dr Natalia Alvarez as our guest for this CSD Educators blog. This is actually a welcome back, as Natalia was a guest editor for the CCDC in 2016, talking about the OpenLab in Uruguay. In this blog instead, Natalia will talk to us about her journey in crystallography, how she first met the CSD (spoiler: it was not love at first sight!), her contribution in regional crystallography schools with insights on how to teach the use of crystallographic databases, in particular the CSD.

When I first met Natalia last year, at the 3rd LACA School on Small Molecule Crystallography, I immediately noticed not only her passion and enthusiasm for crystallography and the CSD, but also her commitment, shared with the rest of the organising committee, to ensure the students would make the most of the experience, adapting the teaching to a virtual environment. And I believe this comes through in her blog. 


A little about my own journey in crystallography

First of all, I would like to say that I feel honored by the opportunity to share my personal experience through this platform. When Ilaria first suggested it after just having finished the first Latin American Crystallography Association (LACA) School on Small Molecule Crystallography that was a 100% online, I felt so tired that I said yes and didn't think on how hard it could be to actually write it. I am generally accused of having an “easy yes”. But here I am and I hope you enjoy and feel encouraged to dive on the use of CSD on all levels of education.

I first fell in love with crystallography back in July 2010 when I attended the ACA's summer school. At that time I was a third year undergrad with little to no clue of what that word meant. My world was blown, I came back to Uruguay thinking I want to do this for the rest of my life. Of course it wasn't that easy, the single crystal diffractometer in Uruguay was broken, there was no evidence of being able to afford a new one in the near future, it just seemed unreachable. Luckily, circumstances changed.

With the arrival of a single crystal diffractometer in 2014, Uruguay hosted an openlab. I attended as a student on that one and became a part of the organizing team by the next one. I felt at home with the regional crystallographic community, so open so eager to share the knowledge, laboratory capabilities, experience, I started attending regional congresses, and even witnessed the foundation of the Latin American Crystallographic Association (LACA) in which I now proudly take part in.

I must confess that I didn't like the CSD that much at first. Prof. Ellena, from the University of Sao Paulo and my thesis co-advisor, kept insisting on my visits to his lab that I should use it, validate my structures, research on similar compounds to those I was working on (coordination compounds aimed for pharmacological use). Of course I could see the potential, but back then when you had a metal in the middle of the molecule it complicated things in Mogul. I kept exploring, the CSD software kept evolving and I can honestly say that nowadays we are really good friends.


Teaching the use of crystallographic databases in crystallography schools

The need to address the potential and benefits that come from using a responsibly curated and enormous database as the CSD when we teach crystallography to young researches is undeniable. Particularly in Latin America a significant percentage of the countries do not have access to the database, mostly because of economic reasons. When organizing a regional school you can count on at least a 30 to 50% of the participants having their first interaction with the software during the school. Luckily, the CCDC has always been open and supportive when it comes to teaching the use of the database. Temporary licenses and access to the software make it possible for participants to really explore the software on their own terms (ed: in 2017 the CCDC also launched it's FAIRE programme to provide longer-term access to the CSD to academics in countries where economic reasons might otherwise restrict access).

I am part of a growing group of crystallographers organizing regional small molecule crystallography schools, mainly 2014 and 2016 Openlab (ed: read the dedicated blog here), 2018 and 2020 LACA school. Having recognized the need to teach the tools the CSD has to offer we started dedicating a two-hour double session to it. During the first two hours there is always an introduction to structural databases in general, with emphasis on the CSD, how it works, what programs does the software package contains, and what can be done with mostly ConQuest, Mercury and EnCIFer. The second session, a practical one, is the one that has evolved more as years passed. On the Openlabs and the 2018 LACA School the practical session was mostly dedicated to case studies, pre-prepared, and a fraction of the time was left to explore with your own structures. This last part is the one that keeps the audience more engaged being part of the process, taking ownership of their work, and this was possible since all were "bring your own crystal" kind of schools. When preparing for the virtual school we mixed it up. We kept the first session mostly unchanged but for the second part we decided to split in smaller groups and having each group decide on a structure to work with and an analytical study to perform to be presented at the end to the rest of the participants. The results were, as expected, surprising. All groups decided on different things to study on the molecule they had chosen, making it super rich in the sharing part of the session. By introducing the presentations to their peers the level of compromise with the task is higher. We were able to see people working with simple aspects as measuring distances and angles, calculating symmetry elements to more complex ones like developing Aromatic Analysis depending on the function of the chosen molecule. Most importantly, this last section enabled the opportunity of learning from each other. I strongly feel that as educators we must encourage students to take responsibility on their own process of learning.

Even though most of us were overwhelmed by having to adapt so rapidly to virtual environments in teaching as a consequence of the pandemic, having to go 100% virtual for the last school ended up being an advantage on a couple of fronts. We were able to reach a wider range of nationalities of the participants and it was the first time that the “theoretical” session of the database was given by CSD instructors. Suzanna and Ilaria were amazing, the clarity of the presentation, attention to detail and the openness to answer questions and concerns raised by the participants were definitely highlights of their contribution.


Final remarks

If you haven't yet submerged into the world of teaching structural science using the CSD software I would like to encourage you to. There is a whole community eager to share advice and ideas in which you can count on if you are beginning this journey. Even though this entry is about the use in crystallography schools we have really good examples of its application in undergrad and grad courses in posts by other colleagues and it is also more than possible to use it in basic chemistry courses in high school. Just take a chance and dive in! The possibilities are endless and only dependent on your imagination.

Group picture of the 3rd LACA School on Small Molecule Crystallography.

Virtual group photo of the for the 3rd LACA School on Small Molecule Crystallography. Top row International Organizing Committee from left to right: Hamilton Napolitano (Universidade Federal de Goiás, Brazil), Vojtech Jancik (Universidad Nacional Autónoma de México, México), Leopoldo Suescun (Universidad de la República, Uruguay), Florencia di Salvo (Universidad de Buenos Aires, Argentina), Javier Ellena (Universidade de São Paulo, Brazil), Natalia Alvarez (Universidad de la República, Uruguay).


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