Help Finding Teaching Materials

Teaching
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I could use some help tracking down materials that use Avogadro for teaching to add to https://two.avogadro.cc/

For example: Yes We Chem

There’s also an online Libre Text that will appear soon, but I know there are many articles published in J Chem. Ed. (and similar journals) that we haven’t tracked.

Here’s a Google Scholar search that can help find articles. It needs some human help, because many articles are about Avogadro’s number or similar concepts, rather than the program.

I’ll post a few links below too.

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Beyond J. Chem. Ed., what are some other journals for chemical education articles?

Chem. Edu. Res. Practice Google Scholar Search

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It likely is too strict to add software as second criterion as the numbers drop from 1090 to now 126 here. On the other hand, without constraint by journal but (fuzzy) requirement of the keywords Avogadro and software alone, Google scholar finds include records e.g. by the Journal of Materials Science, or Journal of Cheminformatics about NWChem and Avogadro as well as Avogadro’s seminal one you co-authored with about 5.5k citations since 2012 (or about 1 publication citing this work for every 25 recorded visitors of the open access publication).

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I think the trick with your search is that the articles tend towards “research use” rather than “teaching in the classroom.”

I agree that it might be nice to have some selection of “interesting articles using Avogadro” although I admit the scope is vast.

Even the scope of “teaching” turns up quite a list as you’ve seen. :slight_smile: I also know of a textbook that is currently in review with Libre Texts.

I have the current list here with the handy “edit this page” option:
https://two.avogadro.cc/teach/articles.html

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Not sure if this is the sort of thing you’re looking for, but I used Avogadro in an introductory course on protein-ligand docking (Welcome to the ScotCHEM protein-ligand docking course — ScotCHEM protein-ligand docking course documentation). The page on creating/modifying ligands uses Avogadro for model building.

It needs to be updated for Avogadro2 though (when I get some time!).

Cheers,
Bruce

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Looks great. Hopefully the update for Avogadro2 eliminates the crashing. :wink:

In all serious, I want to see this too: Auto save feature · Issue #182 · OpenChemistry/avogadroapp · GitHub

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@ghutchis Thanks. The fear of crashing that I instill in my students forces them to get good at saving their work, so I can live with it :wink: (although it’s true that autosave would be nice…)

Actually, although Avogadro2 would work for this course material, the main issue for my reasearch students is the molecular sculpting during optimisation. We deal with some heavily modified peptides with odd stereochemistries, so we still work with old Avogadro so that we can get hands-on during the optimisation. Any idea when it might make it into Avogadro2?

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Real soon™

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The second article states:
“There are other programs that can be used to generate structures of molecules or nanomaterials, including …, Avogadro, …”

So I would say it states the option of using Avogadro, but I wouldn’t say it uses Avogadro for teaching necessarily.

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Which “second article” are you referring to?

Thanks

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The second article of the specific message I was responding to is titled:

“A Simplified Method for the 3D Printing of Molecular Models for Chemical Education 1”

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Hi, Here is a link to the LibreText Book Understanding Organic Chemistry Using Computation. It is written to perform necessary calculations using Orca while the visualization is done with Avogadro 1. I’m currently working on adapting the book to Orca 6 and Avogadro 2. If you have any suggestions please let me know. Understanding Organic Chemistry Through Computation (Boaz and Pearce) - Chemistry LibreTexts

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Please let us know if you have suggestions as we (I) finish up Avogadro 2.

I’ll add the text to the list. Are you looking for suggestions / edits / help as you update it?

One suggestion might be use of xtb - I’ll be putting out an Avogadro + XTB bundle soon, including the plugin from @matterhorn103 - we’re building around it here at Pitt for teaching purposes.

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