Submitted by Anthony L. Fernandez / Merrimack College on Thu, 01/18/2018 - 12:07
My Notes

Students are confronted with a number of new types of isomerism as they move from organic chemistry into inorganic chemistry. This can be confusing and students often have trouble visualizing structures and differentiating between isomers. In this exercise, students are asked to examine a number of different crystal structures from the Teaching Subset (distributed with Mercury version 3.10, early 2018) of the Cambridge Structural Database. Students have to identify the type of isomerism (geometric, linkage, or optical) exhibited by a complex and then identify the specific isomer (cis/trans, mer/fac, R/S, etc.) observed in the structure.

Learning Goals

After completing this exercise, students should be able to:

  • access structures from the CCDC using their web-based form,
  • visualize the structures using Mercury or other viewer,
  • identify the type of isomerism observed in a structure, and
  • determine the correct form of the isomer (e.g. cis or trans).
Equipment needs

A computer is required to access the Teaching Subset of the Cambridge Structural Database in one of the following ways.

  1. The freely available viewer (Mercury) can be downloaded from the CCDC []. The CSD Teaching Subset is included with this download.
  2. Students may also access the structures online from the Cambridge Crystallographic Date Centre. Structures can be accessed via a web-based form [] or via the Teaching Subset page on the CCDC website []. These pages also work on a tablet.
Implementation Notes

I have used this exercise as an in-class exercise and and out-of-class assignment and it works equally well in both formats. If this is one of the first times that your students will be using Mercury, then I would suggest employing this as an in-class activity. While in class, I have students work in pairs to complete this exercise.

I usually send out the spreadsheet and have students enter their responses and then return the spreadsheet to me. I have also pushed this out as a Google Sheet and had them fill it out online. I find that it is easier to keep track when using the Google Sheet. (We are a Google campus so I am guaranteed that all of my students have a Google account and can access the G Suite of programs.) If you would like the Google Sheet version of this exercise, please contact me and I will share it with you.

In the spreadsheet, there is a sheet titled "Drop-down list info" and the information on this sheet populates the drop-down lists in the "Isomerism" sheet. This sheet needs to be present for the drop-down lists to work.  I usually hide this sheet before distributing the file to my students and I have included instructions how to do this on the sheet.

Time Required
30 minutes


Evaluation Methods

Although students submit their answers in the spreadsheet, I do not grade their answers becuase they worked on this exercise in groups. I usually move through the class and interact with the groups to see how they are progressing.

Evaluation Results

This is a relatively simple exercise and students have little trouble coming up with the correct answers for these structures. They sometimes have an issue determining the names of the linkage isomers, especially for the SCN- ligand.

Creative Commons License
Attribution, Non-Commercial, Share Alike CC BY-NC-SA
Sheila Smith / University of Michigan- Dearborn

Anthony, this was exactly what I needed on this snowy-icy  morning when half my small class couldn't make it to campus.  We discussed the differnt types of isomerism in class with a bit of review, and I sent them home to work on this over the weeknd.  I'll let you know how it goes.



Wed, 02/13/2019 - 11:09 Permalink
Anthony L. Fernandez / Merrimack College

Thanks for letting me know Sheila! I woud appreciate any comments that you or you students have...

Wed, 02/13/2019 - 14:30 Permalink
Dominique TOLEDO / UFRO

Hi Anthony!

I would like to try this activity with my students.

Please, can you share the Google Sheet of this exercise?

Thanks in advance


Fri, 11/18/2022 - 21:25 Permalink
Dean Johnston / Otterbein University

Great activity - my students really enjoyed it!

One (rather minor) comment. The last structure, FAMZEZ, an [Os(phen)3]2+ salt, is a racemate, so both isomers (enantiomers) will be present in the unit cell. WebCSD and Mercury will only show one molecule, and that is the the molecule that is shown in the answer key. My students noticed that the name shown in WebCSD was rac-tris(1,10-Phenanthroline)-osmium(ii) bis(hexafluorophosphate.

Another entry in the teaching subset is FAJXOE, which is the same salt, but enantiomerically pure and crystallizing in P212121. It is the lambda form. A disadvantage of this is of course that WebCSD will show the name, including the enantiomeric designation.

Fri, 03/31/2023 - 10:58 Permalink
Anthony L. Fernandez / Merrimack College

Thanks, Dean! 

Yes, your students were good to notice that. I chose FAMZEZ for that reason. You can actually see both enantiomers if you display a 1x1x1 unit cell. I have my students do this, but I forgot to add the note to the VIPEr file. I will update it.

I use the pure isomer (FAJXOE) on exams. 

Given your and your students input, I may change the activity slightly to use FAJXOE and then extend the question by asking the students to look at FAMZEZ. I will think about the best way to do this and will let you know when the LO is updated.

Fri, 03/31/2023 - 14:19 Permalink